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Kindaichi, T., T. Awata, K. Tanabe, N. Ozaki, and A. Ohashi. "Enrichment of marine anammox bacteria in Hiroshima Bay sediments." Water Science and Technology 63, no. 5 (March 1, 2011): 964–69. http://dx.doi.org/10.2166/wst.2011.277.
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Anaerobic ammonium oxidation (anammox) involves the microbiological oxidation of ammonium with nitrite as the electron acceptor and dinitrogen gas as the main product. The Scalindua species, an anammox genus that dominates natural habitats, plays an important role in catalysing the loss of nitrogen from marine environments. Until now, a few Scalindua species have been reported to be enriched from sea sediments. The objective of this study is to enrich marine anammox bacteria with coastal sediments in Hiroshima Bay as the inocula. The enrichment was achieved using a continuous upflow column reactor with synthetic sea water containing ammonium and nitrite. After 48 days of incubation, a simultaneous decrease in ammonium and nitrite was observed. A total nitrogen removal rate of 1.16 kg-N m−3 day−1 was attained after 306 days of incubation when the nitrogen loading rate was 1.32 kg-N m−3 day−1. Phylogenetic analysis revealed that the sequence similarity between the marine anammox-like bacteria in this reactor and the unidentified Candidatus Scalindua sp. was 96–98%. We successfully enriched marine anammox bacteria in the sediments of Hiroshima Bay by using synthetic sea water. Further studies are needed to investigate the characteristics of marine anammox bacteria, including optimal pH, temperature, and nitrogen loading rate.
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Hu, Bao-lan, Li-dong Shen, Xiang-yang Xu, and Ping Zheng. "Anaerobic ammonium oxidation (anammox) in different natural ecosystems." Biochemical Society Transactions 39, no. 6 (November 21, 2011): 1811–16. http://dx.doi.org/10.1042/bst20110711.
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Anammox (anaerobic ammonium oxidation), which is a reaction that oxidizes ammonium to dinitrogen gas using nitrite as the electron acceptor under anoxic conditions, was an important discovery in the nitrogen cycle. The reaction is mediated by a specialized group of planctomycete-like bacteria that were first discovered in man-made ecosystems. Subsequently, many studies have reported on the ubiquitous distribution of anammox bacteria in various natural habitats, including anoxic marine sediments and water columns, freshwater sediments and water columns, terrestrial ecosystems and some special ecosystems, such as petroleum reservoirs. Previous studies have estimated that the anammox process is responsible for 50% of the marine nitrogen loss. Recently, the anammox process was reported to account for 9–40% and 4–37% of the nitrogen loss in inland lakes and agricultural soils respectively. These findings indicate the great potential for the anammox process to occur in freshwater and terrestrial ecosystems. The distribution of different anammox bacteria and their contribution to nitrogen loss have been described in different natural habitats, demonstrating that the anammox process is strongly influenced by the local environmental conditions. The present mini-review summarizes the current knowledge of the ecological distribution of anammox bacteria, their contribution to nitrogen loss in various natural ecosystems and the effects of major influential factors on the anammox process.
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Kawagoshi, Y., Y. Nakamura, H. Kawashima, K. Fujisaki, K. Furukawa, and A. Fujimoto. "Enrichment of marine anammox bacteria from seawater-related samples and bacterial community study." Water Science and Technology 61, no. 1 (January 1, 2010): 119–26. http://dx.doi.org/10.2166/wst.2010.796.
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Anaerobic ammonium oxidation (anammox) is a novel nitrogen pathway catalyzed by anammox bacteria which are obligate anaerobic chemoautotrophs. In this study, enrichment culture of marine anammox bacteria (MAAOB) from the samples related to seawater was conducted. Simultaneous removal of ammonium and nitrite was confirmed in continuous culture inoculated with sediment of a sea-based waste disposal site within 50 days. However, no simultaneous nitrogen removal was observed in cultures inoculated with seawater-acclimated denitrifying sludge or with muddy sediment of tideland even during 200 days. Nitrogen removal rate of 0.13 kg/m3/day was achieved at nitrogen loading rate of 0.16 kg/m3/day after 320th days in the culture inoculated with the sediment of waste disposal site. The nitrogen removal ratio between ammonium nitrogen and nitrite nitrogen was 1:1.07. Denaturing gradient gel electrophoresis (DGGE) analysis indicated that an abundance of the bacteria close to MAAOB and coexistence of ammonium oxidizing bacteria and denitrifying bacteria in the culture.
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Rush, Darci, Helen M. Talbot, Marcel T. J. van der Meer, Ellen C. Hopmans, Ben Douglas, and Jaap S. Sinninghe Damsté. "Biomarker evidence for the occurrence of anaerobic ammonium oxidation in the eastern Mediterranean Sea during Quaternary and Pliocene sapropel formation." Biogeosciences 16, no. 12 (June 19, 2019): 2467–79. http://dx.doi.org/10.5194/bg-16-2467-2019.
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Abstract. The eastern Mediterranean Sea sedimentary record is characterised by intervals of organic-rich sapropel sediments, indicating periods of severe anoxia triggered by astronomical forcing. It has been hypothesised that nitrogen fixation was crucial in injecting the Mediterranean Sea with bioavailable nitrogen (N) during sapropel events. However, the evolution of the N biogeochemical cycle of sapropels is poorly understood. For example, the role of the complementary removal reactions like anaerobic ammonium oxidation (anammox) has not been investigated because the traditional lipid biomarkers for anammox, ladderane fatty acids, are not stable over long periods in the sedimentary record. Using an alternative lipid biomarker for anammox, bacteriohopanetetrol stereoisomer (BHT isomer), we present here for the first time N removal throughout the progression, e.g. formation, propagation, and termination, of basin-wide anoxic events. BHT isomer and ladderanes were analysed in sapropel records taken from three eastern Mediterranean sediment cores, spanning S1 to Pliocene sapropels. Ladderanes were rapidly degraded in sediments, as recently as the S5 sapropel. BHT isomer, however, was present in all sapropel sediments, as far back as the Pliocene, and clearly showed the response of anammox bacteria to marine water column redox shifts in high-resolution records. Two different N removal scenarios were observed in Mediterranean sapropels. During S5, anammox experienced Black Sea-type water column conditions, with the peak of BHT isomer coinciding with the core of the sapropel. Under the alternative scenario observed in the Pliocene sapropel, the anammox biomarker peaked at onset and termination of said sapropel, which may indicate sulfide inhibition of anammox during the core of sapropel deposition. This study shows the use of BHT isomer as a biomarker for anammox in the marine sediment record and highlights its potential in reconstructing anammox during past anoxic events that are too old for ladderanes to be applied, e.g. the history of oxygen minimum zone expansion and oceanic anoxic events.
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Rattray, Jayne E., Jack van de Vossenberg, Andrea Jaeschke, Ellen C. Hopmans, Stuart G. Wakeham, Gaute Lavik, Marcel M. M. Kuypers, et al. "Impact of Temperature on Ladderane Lipid Distribution in Anammox Bacteria." Applied and Environmental Microbiology 76, no. 5 (January 4, 2010): 1596–603. http://dx.doi.org/10.1128/aem.01796-09.
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ABSTRACT Anaerobic ammonium-oxidizing (anammox) bacteria have the unique ability to synthesize fatty acids containing linearly concatenated cyclobutane rings, termed “ladderane lipids.” In this study we investigated the effect of temperature on the ladderane lipid composition and distribution in anammox enrichment cultures, marine particulate organic matter, and surface sediments. Under controlled laboratory conditions we observed an increase in the amount of C20 [5]-ladderane fatty acids compared with the amount of C18 [5]-ladderane fatty acids with increasing temperature and also an increase in the amount of C18 [5]-ladderane fatty acids compared with the amount of C20 [5]-ladderane fatty acids with decreasing temperature. Combining these data with results from the natural environment showed a significant (R 2 = 0.85, P = <0.0001, n = 121) positive sigmoidal relationship between the amounts of C18 and C20 [5]-ladderane fatty acids and the in situ temperature; i.e., there is an increase in the relative abundance of C18 [5]-ladderane fatty acids at lower temperatures and vice versa, particularly at temperatures between 12�C and 20�C. Novel shorter (C16) and longer (C22 to C24) ladderane fatty acids were also identified, but their relative amounts were small and did not change with temperature. The adaptation of ladderane fatty acid chain length to temperature changes is similar to the regulation of common fatty acid composition in other bacteria and may be the result of maintaining constant membrane fluidity under different temperature regimens (homeoviscous adaptation). Our results can potentially be used to discriminate between the origins of ladderane lipids in marine sediments, i.e., to determine if ladderanes are produced in situ in relatively cold surface sediments or if they are fossil remnants originating from the warmer upper water column.
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Rush, D., E. C. Hopmans, S. G. Wakeham, S. Schouten, and J. S. Sinninghe Damsté. "Occurrence and distribution of ladderane oxidation products in different oceanic regimes." Biogeosciences 9, no. 7 (July 4, 2012): 2407–18. http://dx.doi.org/10.5194/bg-9-2407-2012.
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Abstract. Ladderane fatty acids are commonly used as biomarkers for bacteria involved in anaerobic ammonium oxidation (anammox). These lipids have been experimentally shown to undergo aerobic microbial degradation to form short chain ladderane fatty acids. However, nothing is known of the production or the distribution of these oxic biodegradation products in the natural environment. In this study, we analysed marine water column particulate matter and sediment from three different oceanic regimes for the presence of ladderane oxidation products (C14 ladderane fatty acids) and of original ladderane fatty acids (C18 and C20 ladderane fatty acids). We found that ladderane oxidation products, i.e. C14 ladderane fatty acids, are already produced within the water column of the Arabian Sea oxygen minimum zone (OMZ) and thus only low amounts of oxygen (< 3 μM) are needed for the β-oxidation of original ladderane fatty acids to proceed. However, no short chain ladderane fatty acids were detected in the Cariaco Basin water column, where oxygen concentrations were below detection limit, suggesting that the β-oxidation pathway is inhibited by the absence of molecular oxygen, or that the microbes performing the degradation are not proliferating under these conditions. Comparison of distributions of ladderane fatty acids indicates that short chain ladderane fatty acids are mostly produced in the water column and at the sediment surface, before being preserved deeper in the sediments. Short chain ladderane fatty acids were abundant in Arabian Sea and Peru Margin sediments (ODP Leg 201), often in higher concentrations than the original ladderane fatty acids. In a sediment core taken from within the Arabian Sea OMZ, short chain ladderanes made up more than 90% of the total ladderanes at depths greater than 5 cm below sea floor. We also found short chain ladderanes in higher concentrations in hydrolysed sediment residues compared to those freely occurring in lipid extracts, suggesting that they had become bound to the sediment matrix. Furthermore, these matrix-bound short chain ladderanes were found at greater sediment depths than short chain ladderanes in the lipid extract, suggesting that binding to the sediment matrix aids the preservation of these lipids. Though sedimentary degradation of short chain ladderane fatty acids did occur, it appeared to be at a slower rate than that of the original ladderane fatty acids, and short chain ladderane fatty acids were found in sediments from the Late Pleistocene (~ 100 kyr). Together these results suggest that the oxic degradation products of ladderane fatty acids may be suitable biomarkers for past anammox activity in OMZs.
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Rush, D., E. C. Hopmans, S. G. Wakeham, S. Schouten, and J. S. Sinninghe Damsté. "Occurrence and distribution of ladderane oxidation products in different oceanic regimes." Biogeosciences Discussions 9, no. 3 (March 1, 2012): 2343–74. http://dx.doi.org/10.5194/bgd-9-2343-2012.
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Abstract. Ladderane fatty acids have been used to trace bacteria involved in anaerobic ammonium oxidation (anammox). These lipids have been experimentally shown to undergo aerobic microbial degradation to form short chain ladderane fatty acids. However, nothing is known of the production or the distribution of these oxic biodegradation products in the natural environment. In this study, we analysed marine water column particulate matter and sediment from three different oceanic regimes for the presence of ladderane oxidation products (C14 ladderane fatty acids) and of the original ladderane fatty acids (C18 and C20 ladderane fatty acids). We found that short chain ladderane fatty acids are already produced within the water column of the Arabian Sea oxygen minimum zone (OMZ) and thus only low amounts of oxygen (<3 μM) are needed for the β-oxidation of original ladderane fatty acids to proceed. However, no short chain ladderane fatty acids were detected in the Cariaco Basin water column, where oxygen concentrations were below detection limit, suggesting that the β-oxidation pathway is inhibited by the absence of molecular oxygen. Comparison of distributions of ladderane fatty acids indicates that short chain ladderane fatty acids are mostly produced in the water column and at the sediment surface, before being preserved deeper in the sediments. Short chain ladderane fatty acids were abundant in Arabian Sea and Peru Margin sediments (ODP Leg 201), often in higher concentrations than the original ladderane fatty acids. In a sediment core taken from within the Arabian Sea OMZ, short chain ladderanes made up more than 90 % of the total ladderanes at depths greater than 5 cm below sea floor. We also found short chain ladderanes in higher concentrations in hydrolysed sediment residues compared to those freely occurring in lipid extracts, suggesting that they had become bound to the sediment matrix. Furthermore, these matrix-bound short chain ladderanes were found at greater sediment depths than short chain ladderanes in the lipid extract, suggesting that binding to the sediment matrix aids the preservation of these lipids. Though sedimentary degradation of short chain ladderane fatty acids did occur, it appeared to be at a slower rate than that of the original ladderane fatty acids. Together these results suggest that the oxic degradation products of ladderane fatty acids may be suitable biomarkers for past anammox activity in OMZs.
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Lee, Kee Hwan, Chang Hwan Kim, Chan Hong Park, Kiho Yang, Sang Hoon Lee, In Soo Lee, You Jin Kwack, Jae Woo Kwak, Jaewoo Jung, and Jinwook Kim. "Microbial Diversity Responding to Changes in Depositional Conditions during the Last Glacial and Interglacial Period: NE Ulleung Basin, East Sea (Sea of Japan)." Minerals 10, no. 3 (February 26, 2020): 208. http://dx.doi.org/10.3390/min10030208.
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Microbial interaction with minerals are significantly linked with depositional conditions during glacial and interglacial periods, providing a unique redox condition in the sedimentary process. Abiotic geophysical and geochemical properties, including sedimentary facies, magnetic susceptibility, grain size, clay mineralogy, and distribution of elemental compositions in the sediments, have been widely used to understand paleo-depositional environments. In this study, microbial abundance and diversity in the core sediments (6.7 m long) from the northeastern slope of Dokdo Island were adapted to characterize the conventionally defined sedimentary depositional units and conditions in light of microbial habitats. The units of interglacial (Unit 1, <11.5 ka) and late glacial (Unit 2, 11.5–14.5 ka) periods in contrast to the glacial period (Unit 3, >14.5 ka) were distinctively identified in the core, showing a sharp boundary marked by the laminated Mn-carbonate (CaM) mud between bioturbated (Unit 1 and 2) and laminated mud (Unit 3). Based on the marker beds and the occurrence of sedimentary facies, core sediments were divided into three units, Unit 1 (<11.5 ka, interglacial), Unit 2 (11.5–14.5 ka, late glacial), and Unit 3 (>14.5 ka, glacial), in descending order. The sedimentation rate (0.073 cm/year), which was three times higher than the average value for the East Sea (Sea of Japan) was measured in the late glacial period (Unit 2), indicating the settlement of suspended sediments from volcanic clay in the East Sea (Sea of Japan), including Doldo Island. The Fe and Mg-rich smectite groups in Unit 2 can be transported from volcanic sediments, such as from the volcanic island in the East Sea or the east side of Korea, while the significant appearance of the Al-rich smectite group in Unit 1 was likely transported from East China by the Tsushima Warm Current (TWC). The appearance of CaM indicates a redox condition in the sedimentary process because the formation of CaM is associated with an oxidation of Mn2+ forming Mn-oxide in the ocean, and a subsequent reduction of Mn-oxide occurred, likely due to Mn-reducing bacteria resulting in the local supersaturation of Mn2+ and the precipitation of CaM. The low sea level (−120 m) in the glacial period (Unit 3) may restrict water circulation, causing anoxic conditions compared to the late glacial period (Unit 2), inducing favorable redox conditions for the formation of CaM in the boundary of the two units. Indeed, Planctomycetaceae, including anaerobic ammonium oxidation (ANAMMOX) bacteria capable of oxidizing ammonium coupled with Mn-reduction, was identified in the CaM layer by Next Generation Sequencing (NGS). Furthermore, the appearance of aerobic bacteria, such as Alphaproteobacteria, Gammaproteobacteria, and Methylophaga, tightly coupled with the abundance of phytoplankton was significantly identified in Unit 1, suggesting open marine condition in the interglacial period. Bacterial species for each unit displayed a unique grouping in the phylogenetic tree, indicating the different paleo-depositional environments favorable for the microbial habitats during the glacial and interglacial periods.
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Brüchert, Volker, Lisa Bröder, Joanna E. Sawicka, Tommaso Tesi, Samantha P. Joye, Xiaole Sun, Igor P. Semiletov, and Vladimir A. Samarkin. "Carbon mineralization in Laptev and East Siberian sea shelf and slope sediment." Biogeosciences 15, no. 2 (January 25, 2018): 471–90. http://dx.doi.org/10.5194/bg-15-471-2018.
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Abstract. The Siberian Arctic Sea shelf and slope is a key region for the degradation of terrestrial organic material transported from the organic-carbon-rich permafrost regions of Siberia. We report on sediment carbon mineralization rates based on O2 microelectrode profiling; intact sediment core incubations; 35S-sulfate tracer experiments; pore-water dissolved inorganic carbon (DIC); δ13CDIC; and iron, manganese, and ammonium concentrations from 20 shelf and slope stations. This data set provides a spatial overview of sediment carbon mineralization rates and pathways over large parts of the outer Laptev and East Siberian Arctic shelf and slope and allows us to assess degradation rates and efficiency of carbon burial in these sediments. Rates of oxygen uptake and iron and manganese reduction were comparable to temperate shelf and slope environments, but bacterial sulfate reduction rates were comparatively low. In the topmost 50 cm of sediment, aerobic carbon mineralization dominated degradation and comprised on average 84 % of the depth-integrated carbon mineralization. Oxygen uptake rates and anaerobic carbon mineralization rates were higher in the eastern East Siberian Sea shelf compared to the Laptev Sea shelf. DIC ∕ NH4+ ratios in pore waters and the stable carbon isotope composition of remineralized DIC indicated that the degraded organic matter on the Siberian shelf and slope was a mixture of marine and terrestrial organic matter. Based on dual end-member calculations, the terrestrial organic carbon contribution varied between 32 and 36 %, with a higher contribution in the Laptev Sea than in the East Siberian Sea. Extrapolation of the measured degradation rates using isotope end-member apportionment over the outer shelf of the Laptev and East Siberian seas suggests that about 16 Tg C yr−1 is respired in the outer shelf seafloor sediment. Of the organic matter buried below the oxygen penetration depth, between 0.6 and 1.3 Tg C yr−1 is degraded by anaerobic processes, with a terrestrial organic carbon contribution ranging between 0.3 and 0.5 Tg yr−1.
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Bertics, V. J., C. R. Löscher, I. Salonen, A. W. Dale, J. Gier, R. A. Schmitz, and T. Treude. "Occurrence of benthic microbial nitrogen fixation coupled to sulfate reduction in the seasonally hypoxic Eckernförde Bay, Baltic Sea." Biogeosciences 10, no. 3 (March 1, 2013): 1243–58. http://dx.doi.org/10.5194/bg-10-1243-2013.
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Abstract. Despite the worldwide occurrence of marine hypoxic regions, benthic nitrogen (N) cycling within these areas is poorly understood and it is generally assumed that these areas represent zones of intense fixed N loss from the marine system. Sulfate reduction can be an important process for organic matter degradation in sediments beneath hypoxic waters and many sulfate-reducing bacteria (SRB) have the genetic potential to fix molecular N (N2). Therefore, SRB may supply fixed N to these systems, countering some of the N lost via microbial processes, such as denitrification and anaerobic ammonium oxidation. The objective of this study was to evaluate if N2 fixation, possibly by SRB, plays a role in N cycling within the seasonally hypoxic sediments from the Eckernförde Bay, Baltic Sea. Monthly samplings were performed over the course of one year to measure nitrogenase activity (NA) and sulfate reduction rates, to determine the seasonal variations in bioturbation (bioirrigation) activity and important benthic geochemical profiles, such as sulfur and N compounds, and to monitor changes in water column temperature and oxygen concentrations. Additionally, at several time points, the active N-fixing community was examined via molecular tools. Integrated rates of N2 fixation (approximated from NA) and sulfate reduction showed a similar seasonality pattern, with highest rates occurring in August (approx. 22 and 880 nmol cm−3 d−1 of N and SO42−, respectively) and October (approx. 22 and 1300 nmol cm−3 d−1 of N and SO42− respectively), and lowest rates occurring in February (approx. 8 and 32 nmol cm−3 d−1 of N and SO42−, respectively). These rate changes were positively correlated with bottom water temperatures and previous reported plankton bloom activities, and negatively correlated with bottom water oxygen concentrations. Other variables that also appeared to play a role in rate determination were bioturbation, bubble irrigation and winter storm events. Molecular analysis demonstrated the presence of nifH sequences related to two known N2 fixing SRB, namely Desulfovibrio vulgaris and Desulfonema limicola, supporting the hypothesis that some of the nitrogenase activity detected may be attributed to SRB. Overall, our data show that Eckernförde Bay represents a complex ecosystem where numerous environmental variables combine to influence benthic microbial activities involving N and sulfur cycling.
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Bertics, V. J., C. R. Löscher, I. Salonen, A. W. Dale, R. A. Schmitz, and T. Treude. "Occurrence of benthic microbial nitrogen fixation coupled to sulfate reduction in the seasonally hypoxic Eckernförde Bay, Baltic Sea." Biogeosciences Discussions 9, no. 6 (June 6, 2012): 6489–533. http://dx.doi.org/10.5194/bgd-9-6489-2012.
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Abstract. Despite the worldwide occurrence of marine hypoxic regions, benthic nitrogen (N) cycling within these areas is poorly understood and it is generally assumed that these areas represent zones of intense fixed N loss from the marine system. Sulfate reduction can be an important process for organic matter degradation in sediments beneath hypoxic waters and many sulfate-reducing bacteria (SRB) have the genetic potential to fix molecular N (N2). Therefore, SRB may supply fixed N to these systems, countering some of the N lost via microbial processes such as denitrification and anaerobic ammonium oxidation. The objective of this study was to evaluate if N2-fixation, possibly by SRB, plays a role in N cycling within the seasonally hypoxic sediments from Eckernförde Bay, Baltic Sea. Monthly samplings were performed over the course of one year to measure N2-fixation and sulfate reduction rates, to determine the seasonal variations in bioturbation (bioirrigation) activity and important benthic geochemical profiles, such as sulfur and N compounds, and to monitor changes in water column temperature and oxygen concentrations. Additionally, at several time points, rates of benthic denitrification were also measured and the active N-fixing community was examined via molecular tools. Integrated rates of N2-fixation and sulfate reduction showed a similar seasonality pattern, with highest rates occurring in August (approx. 22 and 880 nmol cm−3 d−1 of N and SO42−, respectively) and October (approx. 22 and 1300 nmol cm−3 d−1 of N and SO42−, respectively), and lowest rates occurring in February (approx. 8 and 32 nmol cm−3 d−1 of N and SO42−, respectively). These rate changes were positively correlated with bottom water temperatures and previous reported plankton bloom activities, and negatively correlated with bottom water oxygen concentrations. Other variables that also appeared to play a role in rate determination were bioturbation, bubble irrigation and winter storm events. Molecular analysis demonstrated the presence of nifH sequences related to two known N2-fixing SRB, namely Desulfovibrio vulgaris and Desulfonema limicola, supporting the hypothesis that some of the nitrogenase activity detected may be attributed to SRB. Denitrification appeared to follow a similar trend as the other microbial processes and the ratio of denitrification to N2-fixation ranged from 6.8 in August to 1.1 in February, indicating that in February, the two processes are close to being in balance in terms of N loss and N gain. Overall, our data show that Eckernförde Bay represents a complex ecosystem where numerous environmental variables combine to influence benthic microbial activities involving N and sulfur cycling.
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Thamdrup, Bo, and Tage Dalsgaard. "Production of N2 through Anaerobic Ammonium Oxidation Coupled to Nitrate Reduction in Marine Sediments." Applied and Environmental Microbiology 68, no. 3 (March 2002): 1312–18. http://dx.doi.org/10.1128/aem.68.3.1312-1318.2002.
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ABSTRACT In the global nitrogen cycle, bacterial denitrification is recognized as the only quantitatively important process that converts fixed nitrogen to atmospheric nitrogen gas, N2, thereby influencing many aspects of ecosystem function and global biogeochemistry. However, we have found that a process novel to the marine nitrogen cycle, anaerobic oxidation of ammonium coupled to nitrate reduction, contributes substantially to N2 production in marine sediments. Incubations with 15N-labeled nitrate or ammonium demonstrated that during this process, N2 is formed through one-to-one pairing of nitrogen from nitrate and ammonium, which clearly separates the process from denitrification. Nitrite, which accumulated transiently, was likely the oxidant for ammonium, and the process is thus similar to the anammox process known from wastewater bioreactors. Anaerobic ammonium oxidation accounted for 24 and 67% of the total N2 production at two typical continental shelf sites, whereas it was detectable but insignificant relative to denitrification in a eutrophic coastal bay. However, rates of anaerobic ammonium oxidation were higher in the coastal sediment than at the deepest site and the variability in the relative contribution to N2 production between sites was related to large differences in rates of denitrification. Thus, the relative importance of anaerobic ammonium oxidation and denitrification in N2 production appears to be regulated by the availability of their reduced substrates. By shunting nitrogen directly from ammonium to N2, anaerobic ammonium oxidation promotes the removal of fixed nitrogen in the oceans. The process can explain ammonium deficiencies in anoxic waters and sediments, and it may contribute significantly to oceanic nitrogen budgets.
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Rush, Darci, Jaap S. Sinninghe Damsté, Simon W. Poulton, Bo Thamdrup, A. Leigh Garside, Jenaro Acuña González, Stefan Schouten, Mike S. M. Jetten, and Helen M. Talbot. "Anaerobic ammonium-oxidising bacteria: A biological source of the bacteriohopanetetrol stereoisomer in marine sediments." Geochimica et Cosmochimica Acta 140 (September 2014): 50–64. http://dx.doi.org/10.1016/j.gca.2014.05.014.
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Penton, C. Ryan, Allan H. Devol, and James M. Tiedje. "Molecular Evidence for the Broad Distribution of Anaerobic Ammonium-Oxidizing Bacteria in Freshwater and Marine Sediments." Applied and Environmental Microbiology 72, no. 10 (October 2006): 6829–32. http://dx.doi.org/10.1128/aem.01254-06.
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ABSTRACT Previously available primer sets for detecting anaerobic ammonium-oxidizing (anammox) bacteria are inefficient, resulting in a very limited database of such sequences, which limits knowledge of their ecology. To overcome this limitation, we designed a new primer set that was 100% specific in the recovery of ∼700-bp 16S rRNA gene sequences with >96% homology to the “Candidatus Scalindua” group of anammox bacteria, and we detected this group at all sites studied, including a variety of freshwater and marine sediments and permafrost soil. A second primer set was designed that exhibited greater efficiency than previous primers in recovering full-length (1,380-bp) sequences related to “Ca. Scalindua,” “Candidatus Brocadia,” and “Candidatus Kuenenia.” This study provides evidence for the widespread distribution of anammox bacteria in that it detected closely related anammox 16S rRNA gene sequences in 11 geographically and biogeochemically diverse freshwater and marine sediments.
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Freitag, Thomas E., and James I. Prosser. "Community Structure of Ammonia-Oxidizing Bacteria within Anoxic Marine Sediments." Applied and Environmental Microbiology 69, no. 3 (March 2003): 1359–71. http://dx.doi.org/10.1128/aem.69.3.1359-1371.2003.
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ABSTRACT The potential for oxidation of ammonia in anoxic marine sediments exists through anaerobic oxidation by Nitrosomonas-like organisms, utilizing nitrogen dioxide, coupling of nitrification, manganese reduction, and anaerobic oxidation of ammonium by planctomycetes (the Anammox process). Here we describe the presence of microbial communities with the potential to carry out these processes in a natural marine sediment system (Loch Duich, Scotland). Natural microbial communities of Planctomycetales-Verrucomicrobia and β- and γ-proteobacterial ammonia-oxidizing bacteria were characterized by analysis of 16S rRNA genes amplified using group-specific primers by PCR- and reverse transcription-PCR amplification of 16S rDNA and RNA, respectively. Amplification products were analyzed by sequencing of clones and by denaturant gradient gel electrophoresis (DGGE). Amplification of primers specific for Planctomycetales-Verrucomicrobia and β-proteobacterial ammonia-oxidizing bacteria generated products at all sampling sites and depths, but no product was generated using primers specific for γ-proteobacterial ammonia-oxidizing bacteria. 16S rDNA DGGE banding patterns indicated complex communities of β-proteobacterial ammonia-oxidizing bacteria in anoxic marine sediments. Phylogenetic analysis of sequences from clones and those excised from DGGE gels suggests dominance of Nitrosospira cluster 1-like organisms and of strains belonging to a novel cluster represented in dominant bands in 16S rRNA DGGE banding patterns. Their presence indicates a group of organisms closely related to recognized β-proteobacterial ammonia-oxidizing bacteria that may be selected in anoxic environments and may be capable of anoxic ammonia oxidation. Sequence analysis of planctomycete clone libraries and sequences excised from DGGE gels also demonstrated a diverse microbial community and suggested the presence of new subdivisions, but no sequence related to recognized Anammox organisms was detected.
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Yang, Y., J. Zuo, Z. Quan, S. Lee, P. Shen, and X. Gu. "Study on performance of granular ANAMMOX process and characterization of the microbial community in sludge." Water Science and Technology 54, no. 8 (October 1, 2006): 197–207. http://dx.doi.org/10.2166/wst.2006.812.
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Anaerobic Ammonium Oxidation (ANAMMOX) is a novel biological nitrogen removal process, which is regarded as the most economical process at present. In this paper, two lab-scale UASB reactors, one of which was inoculated with the mixture of anaerobic sludge and aerobic sludge, the other with river sediments, were started up, using the inorganic synthetic water containing ammonium and nitrite as influent. After 421 days' and 356 days operation respectively, the ammonium removal efficiencies in two reactors reached 94% and 86% respectively, the total nitrogen volumetric loading rates were 2.5 and 1.6 kgN/m3.d. ANAMMOX granules were obtained in both reactors; the color of most granules was brown, but some of them were red. Based on the observation and studies on the microstructure of the granules, three kinds of ANAMMOX granular sludge formation mechanisms were proposed: adhering biofilm and disintegrated granular core mechanism, adhering biofilm and inorganic core mechanism and the self-coherence mechanism. For phylogenetic characterization of anaerobic ammonium oxidizers,16S rDNA approach was performed using Planctomycetales-specific PCR amplification. The dominant anammox bacteria occupied more than 90% of Planctomycetales-specific bacteria, and 27% of all bacteria in reactors. The dominant anammox bacteria distantly related to all currently reported candidate anammox genera. Functional gene of amoA was analyzed to investigate the ‘aerobic’ ammonium-oxidizing bacteria in β-Proteobacteria. The ‘aerobic’ ammonium-oxidizing bacteria were more diverse than anammox bacteria, but most of them clustered in anoxic ammonium-oxidizing Nitrosomonas eutropha/europaea groups. The composition of ‘aerobic’ ammonium-oxidizing bacteria is only 2% of all of bacteria in reactors.
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Wijanarka, Wijanarka, Sudarno Sudarno, and Novi A. Pratama. "Pertumbuhan Bakteri Anaerobic Ammonia Oxidation (Anammox) Pada Salinitas 2 dan 9 Persen." JURNAL BIOLOGI PAPUA 9, no. 2 (May 14, 2018): 55–62. http://dx.doi.org/10.31957/jbp.113.
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When ammonia in waste water is lost inappropriately, it will raise an adverse environmental effect for the aquatic cycle. Anammox, anaerobic ammonia oxidation, is a novel process in which nitrite is used as an electron acceptor in the conversion of ammonium to nitrogen gas. The anammox process removes ammonium in the autrotrophic system by leaving little biomass. This study aims to analyze the effect of salinity on the growth of anammox bacteria. The samples used were from the brackish water sediments of the East Flood Canal River of Semarang. The isolation was done by gram staining and the bacteria were inoculated on media with different salinity concentration and the growth was measured using spectrophotometer. The results showed that anammox bacteria had a higher growth rate of 3% (control) when it was grown on a medium with a concentration of 9%. Anammox bacteria grown on anammox selective media showed that the bacteria were able to adapt to environments with different salinity concentrations of 2% and 9%. Key words: anammox, ammonium, nitrogen, anammox bacteria.
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Zhao, Rui, José M. Mogollón, Sophie S. Abby, Christa Schleper, Jennifer F. Biddle, Desiree L. Roerdink, Ingunn H. Thorseth, and Steffen L. Jørgensen. "Geochemical transition zone powering microbial growth in subsurface sediments." Proceedings of the National Academy of Sciences 117, no. 51 (December 7, 2020): 32617–26. http://dx.doi.org/10.1073/pnas.2005917117.
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No other environment hosts as many microbial cells as the marine sedimentary biosphere. While the majority of these cells are expected to be alive, they are speculated to be persisting in a state of maintenance without net growth due to extreme starvation. Here, we report evidence for in situ growth of anaerobic ammonium-oxidizing (anammox) bacteria in ∼80,000-y-old subsurface sediments from the Arctic Mid-Ocean Ridge. The growth is confined to the nitrate–ammonium transition zone (NATZ), a widespread geochemical transition zone where most of the upward ammonium flux from deep anoxic sediments is being consumed. In this zone the anammox bacteria abundances, assessed by quantification of marker genes, consistently displayed a four order of magnitude increase relative to adjacent layers in four cores. This subsurface cell increase coincides with a markedly higher power supply driven mainly by intensified anammox reaction rates, thereby providing a quantitative link between microbial proliferation and energy availability. The reconstructed draft genome of the dominant anammox bacterium showed an index of replication (iRep) of 1.32, suggesting that 32% of this population was actively replicating. The genome belongs to aScalinduaspecies which we nameCandidatus Scalindua sediminis, so far exclusively found in marine sediments. It has the capacity to utilize urea and cyanate and a mixotrophic lifestyle. Our results demonstrate that specific microbial groups are not only able to survive unfavorable conditions over geological timescales, but can proliferate in situ when encountering ideal conditions with significant consequences for biogeochemical nitrogen cycling.
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van Kessel, Maartje A. H. J., Harry R. Harhangi, Gert Flik, Mike S. M. Jetten, Peter H. M. Klaren, and Huub J. M. Op den Camp. "Anammox bacteria in different compartments of recirculating aquaculture systems." Biochemical Society Transactions 39, no. 6 (November 21, 2011): 1817–21. http://dx.doi.org/10.1042/bst20110743.
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Strict environmental restrictions force the aquaculture industry to guarantee optimal water quality for fish production in a sustainable manner. The implementation of anammox (anaerobic ammonium oxidation) in biofilters would result in the conversion of both ammonium and nitrite (both toxic to aquatic animals) into harmless dinitrogen gas. Both marine and freshwater aquaculture systems contain populations of anammox bacteria. These bacteria are also present in the faeces of freshwater and marine fish. Interestingly, a new planctomycete species appears to be present in these recirculation systems too. Further exploitation of anammox bacteria in different compartments of aquaculture systems can lead to a more environmentally friendly aquaculture practice.
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Shcherbakova, V., E. Rivkina, K. Laurinavichuis, S. Pecheritsina, and D. Gilichinsky. "Physiological characteristics of bacteria isolated from water brines within permafrost." International Journal of Astrobiology 3, no. 1 (January 2004): 37–43. http://dx.doi.org/10.1017/s1473550404001806.
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In the Arctic there are lenses of overcooled water brines (cryopegs) sandwiched within permafrost marine sediments 100–120 thousand years old. We have investigated the physiological properties of the pure cultures of anaerobic Clostridium sp. strain 14D1 and two strains of aerobic bacteria Psychrobacter sp. isolated from these cryopegs. The structural and physiological characteristics of new bacteria from water brines have shown their ability to survive and develop under harsh conditions, such as subzero temperatures and high salinity.
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Op den Camp, H. J. M., B. Kartal, D. Guven, L. A. M. P. van Niftrik, S. C. M. Haaijer, W. R. L. van der Star, K. T. van de Pas-Schoonen, et al. "Global impact and application of the anaerobic ammonium-oxidizing (anammox) bacteria." Biochemical Society Transactions 34, no. 1 (January 20, 2006): 174–78. http://dx.doi.org/10.1042/bst0340174.
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In the anaerobic ammonium oxidation (anammox) process, ammonia is oxidized with nitrite as primary electron acceptor under strictly anoxic conditions. The reaction is catalysed by a specialized group of planctomycete-like bacteria. These anammox bacteria use a complex reaction mechanism involving hydrazine as an intermediate. The reactions are assumed to be carried out in a unique prokaryotic organelle, the anammoxosome. This organelle is surrounded by ladderane lipids, which make the organelle nearly impermeable to hydrazine and protons. The localization of the major anammox protein, hydrazine oxidoreductase, was determined via immunogold labelling to be inside the anammoxosome. The anammox bacteria have been detected in many marine and freshwater ecosystems and were estimated to contribute up to 50% of oceanic nitrogen loss. Furthermore, the anammox process is currently implemented in water treatment for the low-cost removal of ammonia from high-strength waste streams. Recent findings suggested that the anammox bacteria may also use organic acids to convert nitrate and nitrite into dinitrogen gas when ammonia is in short supply.
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Fenchel, T. "Methanogenesis in marine shallow water sediments: The quantitative role of anaerobic protozoa with endosymbiotic methanogenic bacteria." Ophelia 37, no. 1 (January 1993): 67–82. http://dx.doi.org/10.1080/00785326.1993.10430378.
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Behrendt, A., D. de Beer, and P. Stief. "Vertical activity distribution of dissimilatory nitrate reduction in coastal marine sediments." Biogeosciences 10, no. 11 (November 21, 2013): 7509–23. http://dx.doi.org/10.5194/bg-10-7509-2013.
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Abstract. The relative importance of two dissimilatory nitrate reduction pathways, denitrification (DEN) and dissimilatory nitrate reduction to ammonium (DNRA), was investigated in intact sediment cores from five different coastal marine field sites (Dorum, Aarhus Bight, Mississippi Delta, Limfjord and Janssand). The vertical distribution of DEN activity was examined using the acetylene inhibition technique combined with N2O microsensor measurements, whereas NH4+ production via DNRA was measured with a recently developed gel probe-stable isotope technique. At all field sites, dissimilatory nitrate reduction was clearly dominated by DEN (59–131% of the total NO3− reduced) rather than by DNRA, irrespective of the sedimentary inventories of electron donors such as organic carbon, sulfide, and iron. Highest ammonium production via DNRA, accounting for up to 8.9% of the total NO3− reduced, was found at a site with very high concentrations of total sulfide and NH4+ within and below the layer in which NO3− reduction occurred. Sediment from two field sites, one with low and one with high DNRA activity in the core incubations, was also used for slurry incubations. Now, in both sediments high DNRA activity was detected accounting for 37–77% of the total NO3− reduced. These contradictory results might be explained by enhanced NO3− availability for DNRA bacteria in the sediment slurries compared to the core-incubated sediments in which diffusion of NO3− from the water column may only reach DEN bacteria, but not DNRA bacteria. The true partitioning of dissimilatory nitrate reduction between DNRA and DEN may thus lie in between the values found in whole core (underestimation of DNRA) and slurry incubations (overestimation of DNRA).
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Awata, Takanori, Katsuichiro Tanabe, Tomonori Kindaichi, Noriatsu Ozaki, and Akiyoshi Ohashi. "Influence of temperature and salinity on microbial structure of marine anammox bacteria." Water Science and Technology 66, no. 5 (September 1, 2012): 958–64. http://dx.doi.org/10.2166/wst.2012.234.
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Anaerobic ammonium oxidation (anammox) is a type of biological oxidation mediated by a group of Planctomycete-like bacteria. Members of the genus Candidatus Scalindua are mainly found in marine environments, but not exclusively. This group is cultured using different inoculums and conditions; however, its optimal growth conditions are not clear. Additionally, little information is known about the factors that influence the activity and the selection of a population of marine anammox bacteria. This study was conducted to investigate the influence of temperature and salinity on the marine anammox community. To accomplish this, an up-flow fixed-bed column reactor was operated, and quantitative fluorescence in situ hybridization (FISH) with probes specific to dominant marine anammox bacteria was conducted. Anammox activity was observed at 20 and 30 °C, but not at 10 °C. A nitrogen removal rate of 0.32 kg TN m–3 day–1 was obtained at 20 °C. These results suggest that temperature affects the activity (nitrogen removal rate) of anammox bacteria, while salinity does not affect the activity in the marine anammox biofilm.
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Li, Meng, Yiguo Hong, Martin Gunter Klotz, and Ji-Dong Gu. "A comparison of primer sets for detecting 16S rRNA and hydrazine oxidoreductase genes of anaerobic ammonium-oxidizing bacteria in marine sediments." Applied Microbiology and Biotechnology 86, no. 2 (January 27, 2010): 781–90. http://dx.doi.org/10.1007/s00253-009-2361-5.
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Zhang, Yaping, Xiaohong Ruan, and Wenli Shi. "Changes in the nitrogen biogeochemical cycle in sediments of an urban river under different dissolved oxygen levels." Water Supply 19, no. 4 (November 26, 2018): 1271–78. http://dx.doi.org/10.2166/ws.2018.188.
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Abstract Urban rivers are considered as a hot spot of microbial nitrogen cycling due to extensive N loading. However, microbial nitrogen transformation dynamics in urban rivers with different dissolved oxygen (DO) conditions are still unclear. This study investigated the effects of DO concentration changes (anaerobic to aerobic) in overlying water on nitrogen-cycling gene abundance in incubation conditions using sediment from a typical urban river in the Yangtze River Delta. Quantitative polymerase chain reaction (qPCR) results revealed that the abundances of the nitrification gene amoA, denitrification gene nirS/K, norB, nosZ, and anammox gene hzo increased by one to two orders of magnitude from anaerobic to aerobic conditions. Ammonia-oxidizing archaea (AOA) predominated the ammonium oxidation microbial populations, about tenfold more than the ammonia-oxidizing bacteria (AOB) populations. Significant correlations were found among the abundances of AOA-amoA, AOB-amoA, nirS, nirK, and hzo genes, implying a close coupling of aerobic ammonium oxidation (AAO), denitrification, and anammox processes at the molecular level. Moreover, the nitrogen transformation rates were calculated using a box model linking the measured dissolved inorganic nitrogen species. The contribution of anammox to N2 production was 85% under saturated treatment, and the AAO rate was significantly positive correlated to the anammox rate. Our results suggested that coupled AAO and anammox might be the dominant pathway for reactive nitrogen removal in urban rivers with elevated DO levels.
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Zhu, Jin, Yan He, Yishuang Zhu, Minsheng Huang, and Yaping Zhang. "Biogeochemical sulfur cycling coupling with dissimilatory nitrate reduction processes in freshwater sediments." Environmental Reviews 26, no. 2 (June 2018): 121–32. http://dx.doi.org/10.1139/er-2017-0047.
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Dissimilatory nitrate reduction processes including denitrification, anaerobic ammonium oxidation (ANAMMOX), and dissimilatory nitrate reduction to ammonium (DNRA) are crucial nitrogen (N) cycling pathways in freshwater ecosystems. Denitrification has long been considered as the primary pathway of N loss from aquatic environments. Recently, ANAMMOX and DNRA have been gaining more attention in N dynamics at the sediment–water interface. The ubiquitous presence of various sulfur (S) species in sediments makes them an important role on N transport. Interactions between dissimilatory nitrate reduction and the S cycle are mainly embodied by the inhibitory or promoting effects of sulfide on nitrate-reducing pathways, as well as the competition of sulfate with nitrate reduction for substrates. This review summarizes the current progress in the coupling of S cycling with nitrate-reducing pathways in freshwater sediments, the distribution and diversity of related microorganisms, as well as the functional genes encoding related enzymes. Future perspectives of related research are discussed in terms of coupled N cycling with other element cycles and molecular detection of functional bacteria to better understand and manipulate N cycling in freshwater environments.
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Araujo, J. C., M. M. S. Correa, E. C. Silva, A. P. Campos, V. M. Godinho, M. Von Sperling, and C. A. L. Chernicharo. "Investigation of aerobic and anaerobic ammonium-oxidising bacteria presence in a small full-scale wastewater treatment system comprised by UASB reactor and three polishing ponds." Water Science and Technology 61, no. 3 (February 1, 2010): 737–43. http://dx.doi.org/10.2166/wst.2010.955.
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This work applied PCR amplification method and Fluorescence in situ hybridisation (FISH) with primers and probes specific for the anammox organisms and aerobic ammonia-oxidising β-Proteobacteria in order to detect these groups in different samples from a wastewater treatment system comprised by UASB reactor and three polishing (maturation) ponds in series. Seven primer pairs were used in order to detect Anammox bacteria. Positive results were obtained with three of them, suggesting that Anammox could be present in polishing pond sediments. However, Anammox bacteria were not detected by FISH, indicating that they were not present in sediment samples, or they could be present but below FISH detection limit. Aerobic ammonia- and nitrite-oxidising bacteria were verified in water column samples through Most Probable Number (MPN) analysis, but they were not detected in sediment samples by FISH. Ammonia removal efficiencies occurred systematically along the ponds (24, 32, and 34% for polishing pond 1, 2, and 3, respectively) but the major reaction responsible for this removal is still unclear. Some nitrification might have occurred in water samples because some nitrifying bacteria were present. Also Anammox reaction might have occurred because Anammox genes were detected in the sediments, but probably this reaction was too low to be noticed. It is important also to consider that some of the ammonia removal observed might be related to NH3 stripping, associated with the pH increase resulting from the intensive photosynthetic activity in the ponds (mechanism under investigation). Therefore, it can be concluded that more than one mechanism (or reaction) might be involved in the ammonia removal in the polishing ponds investigated in this study.
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Dang, Hongyue, Ruipeng Chen, Lin Wang, Lizhong Guo, Pingping Chen, Zuwang Tang, Fang Tian, Shaozheng Li, and Martin G. Klotz. "Environmental Factors Shape Sediment Anammox Bacterial Communities in Hypernutrified Jiaozhou Bay, China." Applied and Environmental Microbiology 76, no. 21 (September 10, 2010): 7036–47. http://dx.doi.org/10.1128/aem.01264-10.
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ABSTRACT Bacterial anaerobic ammonium oxidation (anammox) is an important process in the marine nitrogen cycle. Because ongoing eutrophication of coastal bays contributes significantly to the formation of low-oxygen zones, monitoring of the anammox bacterial community offers a unique opportunity for assessment of anthropogenic perturbations in these environments. The current study used targeting of 16S rRNA and hzo genes to characterize the composition and structure of the anammox bacterial community in the sediments of the eutrophic Jiaozhou Bay, thereby unraveling their diversity, abundance, and distribution. Abundance and distribution of hzo genes revealed a greater taxonomic diversity in Jiaozhou Bay, including several novel clades of anammox bacteria. In contrast, the targeting of 16S rRNA genes verified the presence of only “Candidatus Scalindua,” albeit with a high microdiversity. The genus “Ca. Scalindua” comprised the apparent majority of active sediment anammox bacteria. Multivariate statistical analyses indicated a heterogeneous distribution of the anammox bacterial assemblages in Jiaozhou Bay. Of all environmental parameters investigated, sediment organic C/organic N (OrgC/OrgN), nitrite concentration, and sediment median grain size were found to impact the composition, structure, and distribution of the sediment anammox bacterial community. Analysis of Pearson correlations between environmental factors and abundance of 16S rRNA and hzo genes as determined by fluorescent real-time PCR suggests that the local nitrite concentration is the key regulator of the abundance of anammox bacteria in Jiaozhou Bay sediments.
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Woebken, Dagmar, Bernhard M. Fuchs, Marcel M. M. Kuypers, and Rudolf Amann. "Potential Interactions of Particle-Associated Anammox Bacteria with Bacterial and Archaeal Partners in the Namibian Upwelling System." Applied and Environmental Microbiology 73, no. 14 (May 25, 2007): 4648–57. http://dx.doi.org/10.1128/aem.02774-06.
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ABSTRACT Recent studies have shown that the anaerobic oxidation of ammonium by anammox bacteria plays an important role in catalyzing the loss of nitrogen from marine oxygen minimum zones (OMZ). However, in situ oxygen concentrations of up to 25 μM and ammonium concentrations close to or below the detection limit in the layer of anammox activity are hard to reconcile with the current knowledge of the physiology of anammox bacteria. We therefore investigated samples from the Namibian OMZ by comparative 16S rRNA gene analysis and fluorescence in situ hybridization. Our results showed that “Candidatus Scalindua” spp., the typical marine anammox bacteria, colonized microscopic particles that were likely the remains of either macroscopic marine snow particles or resuspended particles. These particles were slightly but significantly (P < 0.01) enriched in Gammaproteobacteria (11.8% ± 5.0%) compared to the free-water phase (8.1% ± 1.8%). No preference for the attachment to particles could be observed for members of the Alphaproteobacteria and Bacteroidetes, which were abundant (12 to 17%) in both habitats. The alphaproteobacterial SAR11 clade, the Euryarchaeota, and group I Crenarchaeota, were all significantly depleted in particles compared to their presence in the free-water phase (16.5% ± 3.5% versus 2.6% ± 1.7%, 2.7% ± 1.9% versus <1%, and 14.9% ± 4.6% versus 2.2% ± 1.8%, respectively, all P < 0.001). Sequence analysis of the crenarchaeotal 16S rRNA genes showed a 99% sequence identity to the nitrifying “Nitrosopumilus maritimus.” Even though we could not observe conspicuous consortium-like structures of anammox bacteria with particle-enriched bacterioplankton groups, we hypothesize that members of Gammaproteobacteria, Alphaproteobacteria, and Bacteroidetes play a critical role in extending the anammox reaction to nutrient-depleted suboxic water layers in the Namibian upwelling system by creating anoxic, nutrient-enriched microniches.
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Lopez, P., M. Vidal, X. Lluch, and JA Morgui. "Sediment metabolism in a transitional continental - marine area: The Albufera of Majorca (Balearic Islands, Spain)." Marine and Freshwater Research 46, no. 1 (1995): 45. http://dx.doi.org/10.1071/mf9950045.
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The concentrations of nutrients in sediment pore water and the fluxes of nutrients at the water-sediment interface were measured in a channel that joins continental and marine areas in the Albufera of Majorca in order to evaluate the role of sediments in the nutrient dynamics in this system. Upstream, surficial pore water presented lower values of Eh, which became negative in summer, whereas downstream Eh remained positive. Nutrient concentrations were especially high upstream, reaching 1000 mol L-1 of NH4 and 75 μmol L-1 of PO4 during summer. In summer, measured fluxes showed intense respiration upstream, with an oxygen consumption of 130 mg m-2 h-1 and a respiratory quotient near 4, which indicates dominance of anaerobic respiration. Total CO2 efflux and nutrient fluxes were also high, reaching 30.50 mmol m-2 h-1 for CO2, >2000 μmol m-2 h-1 for NH4 and 58 μmol m-2 h-1 for PO4. A substantial amount of the total CO2 efflux (14 mmol m-2 h-1) was due to calcium carbonate redissolution. Downstream, oxygen consumption, respiratory quotient and ammonium fluxes were lower (around 70 mg m-2 h-1, between 2 and 3, and <20 μmol m-2 h-1, respectively), which indicates a moderate rate of decomposition activity and suggests denitrification as the main respiratoy process. Differences between fluxes measured 'in situ' and those calculated from pore-water concentrations indicated non-diffusive fluxes upstream and suggest substantial denitrifying activity downstream. Extra keywords: benthic chambers, sediment fluxes, pore water, ammonium, phosphate.
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Sayama, Mikio. "Presence of Nitrate-Accumulating Sulfur Bacteria and Their Influence on Nitrogen Cycling in a Shallow Coastal Marine Sediment." Applied and Environmental Microbiology 67, no. 8 (August 1, 2001): 3481–87. http://dx.doi.org/10.1128/aem.67.8.3481-3487.2001.
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ABSTRACT Nitrate flux between sediment and water, nitrate concentration profile at the sediment-water interface, and in situ sediment denitrification activity were measured seasonally at the innermost part of Tokyo Bay, Japan. For the determination of sediment nitrate concentration, undisturbed sediment cores were sectioned into 5-mm depth intervals and each segment was stored frozen at −30°C. The nitrate concentration was determined for the supernatants after centrifuging the frozen and thawed sediments. Nitrate in the uppermost sediment showed a remarkable seasonal change, and its seasonal maximum of up to 400 μM was found in October. The directions of the diffusive nitrate fluxes predicted from the interfacial concentration gradients were out of the sediment throughout the year. In contrast, the directions of the total nitrate fluxes measured by the whole-core incubation were into the sediment at all seasons. This contradiction between directions indicates that a large part of the nitrate pool extracted from the frozen surface sediments is not a pore water constituent, and preliminary examinations demonstrated that the nitrate was contained in the intracellular vacuoles of filamentous sulfur bacteria dwelling on or in the surface sediment. Based on the comparison between in situ sediment denitrification activity and total nitrate flux, it is suggested that intracellular nitrate cannot be directly utilized by sediment denitrification, and the probable fate of the intracellular nitrate is hypothesized to be dissimilatory reduction to ammonium. The presence of nitrate-accumulating sulfur bacteria therefore may lower nature's self-purification capacity (denitrification) and exacerbate eutrophication in shallow coastal marine environments.
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Grice, K., R. E. Summons, E. Grosjean, R. J. Twitchett, W. Dunning, S. X. Wang, and M. E. Bottcher. "DEPOSITIONAL CONDITIONS OF THE NORTHERN ONSHORE PERTH BASIN (BASAL TRIASSIC)." APPEA Journal 45, no. 1 (2005): 262. http://dx.doi.org/10.1071/aj04023.
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An oil-source rock correlation has been established for the northern onshore Perth Basin (Western Australia) based on unusual aromatic and polar biomarkers attributed ultimately to a green sulphur bacterial source. Several of these biomarkers have been identified throughout the entire Sapropelic Interval of a proven petroleum source rock intersected within a recently discovered marine Permian- Triassic Perth Basin borehole (Hovea–3) and several Perth Basin crude oils. Today, green sulphur bacteria live in the anaerobic zones of stratified lakes or in marine environments with restricted water circulation, where the upper sulphide limit coincides with the lower limit of oxygen. The presence of photosynthetic pigments and carotenoids of green sulphur bacteria, or their diagenetic alteration products in sediments provide unequivocal evidence for photic zone euxinic conditions in the paleowater column. Multiple lines of evidence for photic zone euxinia and euxinic depositional conditions for the Hovea–3 source rock have been obtained from biomarker analyses. Photic zone euxinia is usually associated with the widespread deposition of organic-matter-rich sediments that constitute important source rocks for petroleum deposits that are being exploited today. With the exception of the Perth Basin, such organic-matter-rich sediments are virtually absent from Upper Permian and Lower Triassic sediments globally. Several lines of evidence indicate localised surface ocean productivity may have played a key role in the deposition of a petroleum source rock at this location, although photic zone euxinia was globally more widespread during the Permian-Triassic Superanoxic Event.
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Rodrigues, V. A. J., E. F. A. Mac Conell, D. F. C. Dias, M. von Sperling, J. C. de Araújo, and J. L. Vasel. "Nitrogen removal in a shallow maturation pond with sludge accumulated during 10 years of operation in Brazil." Water Science and Technology 76, no. 2 (March 31, 2017): 268–78. http://dx.doi.org/10.2166/wst.2017.193.
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Accumulated sludge in polishing (maturation) ponds reduces the hydraulic retention time (smaller useful volume), and this could potentially lead to a decrease in performance. However, settled biomass, present in the sediments, can contribute to nitrogen removal by different mechanisms such as nitrification and denitrification. This study investigated the influence of the bottom sludge present in a shallow maturation pond treating the effluent from an anaerobic reactor on the nitrification and denitrification processes. Nitrification and denitrification rates were determined in sediment cores by applying ammonia pulses. Environmental conditions in the medium were measured and bacteria detected and quantified by real-time polymerase chain reaction (real-time PCR). The pond showed daily cycles of mixing and stratification and most of the bacteria involved in nitrogen removal decreased in concentration from the upper to the lower part of the sludge layer. The results indicate that denitrifiers, nitrifiers and anammox bacteria coexisted in the sludge, and thus different metabolic pathways were involved in ammonium removal in the system. Therefore, the sediment contributed to nitrogen removal, even with a decrease in the hydraulic retention time in the pond due to the volume occupied by the sludge.
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Kushkevych, Ivan, Blanka Hýžová, Monika Vítězová, and Simon K. M. R. Rittmann. "Microscopic Methods for Identification of Sulfate-Reducing Bacteria from Various Habitats." International Journal of Molecular Sciences 22, no. 8 (April 13, 2021): 4007. http://dx.doi.org/10.3390/ijms22084007.
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This paper is devoted to microscopic methods for the identification of sulfate-reducing bacteria (SRB). In this context, it describes various habitats, morphology and techniques used for the detection and identification of this very heterogeneous group of anaerobic microorganisms. SRB are present in almost every habitat on Earth, including freshwater and marine water, soils, sediments or animals. In the oil, water and gas industries, they can cause considerable economic losses due to their hydrogen sulfide production; in periodontal lesions and the colon of humans, they can cause health complications. Although the role of these bacteria in inflammatory bowel diseases is not entirely known yet, their presence is increased in patients and produced hydrogen sulfide has a cytotoxic effect. For these reasons, methods for the detection of these microorganisms were described. Apart from selected molecular techniques, including metagenomics, fluorescence microscopy was one of the applied methods. Especially fluorescence in situ hybridization (FISH) in various modifications was described. This method enables visual identification of SRB, determining their abundance and spatial distribution in environmental biofilms and gut samples.
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Gier, J., S. Sommer, C. R. Löscher, A. W. Dale, R. A. Schmitz, and T. Treude. "Nitrogen fixation in sediments along a depth transect through the Peruvian oxygen minimum zone." Biogeosciences Discussions 12, no. 17 (September 2, 2015): 14401–40. http://dx.doi.org/10.5194/bgd-12-14401-2015.
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Abstract. Benthic nitrogen (N2) fixation and sulfate reduction (SR) were investigated in the Peruvian oxygen minimum zone (OMZ). Sediment samples, retrieved by a multiple corer were taken at six stations (70–1025 m) along a depth transect at 12° S, covering anoxic and hypoxic bottom water conditions. Benthic N2 fixation was detected at all sites, with high rates measured in OMZ mid-waters between the 70 and 253 m and lowest N2 fixation rates below 253 m down to 1025 m water depth. SR rates were decreasing with increasing water depth, with highest rates at the shallow site. Benthic N2 fixation depth profiles largely overlapped with SR depth profiles, suggesting that both processes are coupled. The potential of N2 fixation by SR bacteria was verified by the molecular analysis of nifH genes. Detected nifH sequences clustered with SR bacteria that have been demonstrated to fix N2 in other benthic environments. Depth-integrated rates of N2 fixation and SR showed no direct correlation along the 12° S transect, suggesting that the benthic diazotrophs in the Peruvian OMZ are being controlled by additional various environmental factors. The organic matter availability and the presence of sulfide appear to be major drivers for benthic diazotrophy. It was further found that N2 fixation was not inhibited by high ammonium concentrations. N2 fixation rates in OMZ sediments were similar to rates measured in other organic-rich sediments. Overall, this work improves our knowledge on N sources in marine sediments and contributes to a better understanding of N cycling in OMZ sediments.
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Black, Ellen M., Michael S. Chimenti, and Craig L. Just. "Effect of freshwater mussels on the vertical distribution of anaerobic ammonia oxidizers and other nitrogen-transforming microorganisms in upper Mississippi river sediment." PeerJ 5 (July 12, 2017): e3536. http://dx.doi.org/10.7717/peerj.3536.
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Targeted qPCR and non-targeted amplicon sequencing of 16S rRNA genes within sediment layers identified the anaerobic ammonium oxidation (anammox) niche and characterized microbial community changes attributable to freshwater mussels. Anammox bacteria were normally distributed (Shapiro-Wilk normality test, W-statistic =0.954, p = 0.773) between 1 and 15 cm depth and were increased by a factor of 2.2 (p < 0.001) at 3 cm below the water-sediment interface when mussels were present. Amplicon sequencing of sediment at depths relevant to mussel burrowing (3 and 5 cm) showed that mussel presence reduced observed species richness (p = 0.005), Chao1 diversity (p = 0.005), and Shannon diversity (p < 0.001), with more pronounced decreases at 5 cm depth. A non-metric, multidimensional scaling model showed that intersample microbial species diversity varied as a function of mussel presence, indicating that sediment below mussels harbored distinct microbial communities. Mussel presence corresponded with a 4-fold decrease in a majority of operational taxonomic units (OTUs) classified in the phyla Gemmatimonadetes, Actinobacteria, Acidobacteria, Plantomycetes, Chloroflexi, Firmicutes, Crenarcheota, and Verrucomicrobia. 38 OTUs in the phylum Nitrospirae were differentially abundant (p < 0.001) with mussels, resulting in an overall increase from 25% to 35%. Nitrogen (N)-cycle OTUs significantly impacted by mussels belonged to anammmox genus Candidatus Brocadia, ammonium oxidizing bacteria family Nitrosomonadaceae, ammonium oxidizing archaea genus Candidatus Nitrososphaera, nitrite oxidizing bacteria in genus Nitrospira, and nitrate- and nitrite-dependent anaerobic methane oxidizing organisms in the archaeal family “ANME-2d” and bacterial phylum “NC10”, respectively. Nitrosomonadaceae (0.9-fold (p < 0.001)) increased with mussels, while NC10 (2.1-fold (p < 0.001)), ANME-2d (1.8-fold (p < 0.001)), and Candidatus Nitrososphaera (1.5-fold (p < 0.001)) decreased with mussels. Co-occurrence of 2-fold increases in Candidatus Brocadia and Nitrospira in shallow sediments suggests that mussels may enhance microbial niches at the interface of oxic–anoxic conditions, presumably through biodeposition and burrowing. Furthermore, it is likely that the niches of Candidatus Nitrososphaera and nitrite- and nitrate-dependent anaerobic methane oxidizers were suppressed by mussel biodeposition and sediment aeration, as these phylotypes require low ammonium concentrations and anoxic conditions, respectively. As far as we know, this is the first study to characterize freshwater mussel impacts on microbial diversity and the vertical distribution of N-cycle microorganisms in upper Mississippi river sediment. These findings advance our understanding of ecosystem services provided by mussels and their impact on aquatic biogeochemical N-cycling.
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Chakraborty, Anirban, S. Emil Ruff, Xiyang Dong, Emily D. Ellefson, Carmen Li, James M. Brooks, Jayme McBee, Bernie B. Bernard, and Casey R. J. Hubert. "Hydrocarbon seepage in the deep seabed links subsurface and seafloor biospheres." Proceedings of the National Academy of Sciences 117, no. 20 (April 30, 2020): 11029–37. http://dx.doi.org/10.1073/pnas.2002289117.
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Marine cold seeps transmit fluids between the subseafloor and seafloor biospheres through upward migration of hydrocarbons that originate in deep sediment layers. It remains unclear how geofluids influence the composition of the seabed microbiome and if they transport deep subsurface life up to the surface. Here we analyzed 172 marine surficial sediments from the deep-water Eastern Gulf of Mexico to assess whether hydrocarbon fluid migration is a mechanism for upward microbial dispersal. While 132 of these sediments contained migrated liquid hydrocarbons, evidence of continuous advective transport of thermogenic alkane gases was observed in 11 sediments. Gas seeps harbored distinct microbial communities featuring bacteria and archaea that are well-known inhabitants of deep biosphere sediments. Specifically, 25 distinct sequence variants within the uncultivated bacterial phyla Atribacteria and Aminicenantes and the archaeal order Thermoprofundales occurred in significantly greater relative sequence abundance along with well-known seep-colonizing members of the bacterial genus Sulfurovum, in the gas-positive sediments. Metabolic predictions guided by metagenome-assembled genomes suggested these organisms are anaerobic heterotrophs capable of nonrespiratory breakdown of organic matter, likely enabling them to inhabit energy-limited deep subseafloor ecosystems. These results point to petroleum geofluids as a vector for the advection-assisted upward dispersal of deep biosphere microbes from subsurface to surface environments, shaping the microbiome of cold seep sediments and providing a general mechanism for the maintenance of microbial diversity in the deep sea.
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Hermans, Martijn, Nils Risgaard-Petersen, Filip J. R. Meysman, and Caroline P. Slomp. "Biogeochemical impact of cable bacteria on coastal Black Sea sediment." Biogeosciences 17, no. 23 (December 2, 2020): 5919–38. http://dx.doi.org/10.5194/bg-17-5919-2020.
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Abstract. Cable bacteria can strongly alter sediment biogeochemistry. Here, we used laboratory incubations to determine the potential impact of their activity on the cycling of iron (Fe), phosphorus (P) and sulfur (S). Microsensor depth profiles of oxygen, sulfide and pH in combination with electric potential profiling and fluorescence in situ hybridisation (FISH) analyses showed a rapid development (<5 d) of cable bacteria, followed by a long period of activity (>200 d). During most of the experiment, the current density correlated linearly with the oxygen demand. Sediment oxygen uptake was attributed to the activity of cable bacteria and the oxidation of reduced products from the anaerobic degradation of organic matter, such as ammonium. Pore water sulfide was low (< 5 µM) throughout the experiment. Sulfate reduction acted as the main source of sulfide for cable bacteria. Pore water Fe2+ reached levels of up to 1.7 mM during the incubations, due to the dissolution of FeS (30 %) and siderite, an Fe carbonate mineral (70 %). Following the upward diffusion of Fe2+, a surface enrichment of Fe oxides formed. Hence, besides FeS, siderite may act as a major source of Fe for Fe oxides in coastal surface sediments where cable bacteria are active. Using µXRF, we show that the enrichments in Fe oxides induced by cable bacteria are located in a thin subsurface layer of 0.3 mm. We show that similar subsurface layers enriched in Fe and P are also observed at field sites where cable bacteria were recently active and little bioturbation occurs. This suggests that such subsurface Fe oxide layers, which are not always visible to the naked eye, could potentially be a marker for recent activity of cable bacteria.
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Sun, Bin, Hui Zhao, Yanhong Zhao, Maurice Tucker, Zuozhen Han, and Huaxiao Yan. "Bio-Precipitation of Carbonate and Phosphate Minerals Induced by the Bacterium Citrobacter freundii ZW123 in an Anaerobic Environment." Minerals 10, no. 1 (January 13, 2020): 65. http://dx.doi.org/10.3390/min10010065.
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In this study, a facultative anaerobic strain isolated from marine sediments and identified as Citrobacter freundii, was used to induce the precipitation of carbonate and phosphate minerals in the laboratory under anaerobic conditions. This is the first time that the ability of C. freundii ZW123 to precipitate carbonate and phosphate minerals has been demonstrated. During the experiments, carbonic anhydrase, alkaline phosphatase and ammonium released by the bacteria not only promoted an increase in pH, but also drove the supersaturation and precipitation of carbonate and phosphate minerals. The predominant bio-mediated minerals precipitated at various Mg/Ca molar ratios were calcite, vaterite, Mg-rich calcite, monohydrocalcite and struvite. A preferred orientation towards struvite was observed. Scanning transmission electron microscopy (STEM) and elemental mapping showed the distribution of magnesium and calcium elements within Mg-rich calcite. Many organic functional groups, including C=O, C–O–C and C–O, were detected within the biominerals, and these functional groups were also identified in the associated extracellular polymeric substances (EPS). Fifteen kinds of amino acid were detected in the biotic minerals, almost identical to those of the EPS, indicating a close relationship between EPS and biominerals. Most amino acids are negatively charged and able to adsorb cations, providing an oversaturated microenvironment to facilitate mineral nucleation. The X-ray photoelectron spectroscopy (XPS) spectrum of struvite shows the presence of organic functional groups on the mineral surface, suggesting a role of the microorganism in struvite precipitation. The ZW123 bacteria provided carbon and nitrogen for the formation of the biotic minerals through their metabolism, which further emphasizes the close relationship between biominerals and the microorganisms. Thermal studies showed the enhanced thermal stability of biotic minerals, perhaps due to the participation of the bacteria ZW123. The presence of amino acids such as Asp and Glu may explain the high magnesium content of some calcites. Molecular dynamics simulations demonstrated that the morphological change and preferred orientation were likely caused by selective adsorption of EPS onto the various struvite crystal surfaces. Thus, this study shows the significant role played by C. freundii ZW123 in the bioprecipitation of carbonate and phosphate minerals and provides some insights into the processes involved.
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Kaplan, D., R. Wilhelm, and A. Abeliovich. "Interdependent environmental factors controlling nitrification in waters." Water Science and Technology 42, no. 1-2 (July 1, 2000): 167–72. http://dx.doi.org/10.2166/wst.2000.0309.
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In many areas of the world limited water resources have lead to increased use of recycled water for agricultural and industrial purposes. Prior to releasing reclaimed water to consumers, excessive concentrations of inorganic nitrogenous compounds (ammonium, nitrite and nitrate) must be removed, and the water has to meet sanitary standards. The dynamics and abundance of the different nitrogenous compounds depend on the nitrification process (microbial oxidation of ammonia and nitrite). This is a key process in the nitrogen cycle and the autotrophic nitrifying bacteria catalyzing it are found in soils, sediments, wastewater, freshwater and marine water. Nitrification is a two-step process: first ammonia oxidizers convert ammonia to nitrite and then nitrite oxidizers convert nitrite to nitrate. An efficient nitrification process requires linked balanced activity of the two bacterial groups. Environmental factors that control nitrification affect ammonia and nitrite oxidizers differentially and thus disrupt the linkage between the two steps of the process. The effects of various environmental factors on the two bacterial groups and on the overall nitrification process are discussed. Light was identified to be a major factor inhibiting nitrification in a wastewater reservoir in Israel. Especially, nitrite oxidation was hindered causing the accumulation of nitrite during late spring and summer.
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Zhao, Jian-Shen, Charles W. Greer, Sonia Thiboutot, Guy Ampleman, and Jalal Hawari. "Biodegradation of the nitramine explosives hexahydro-1,3,5-trinitro-1,3,5-triazine and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine in cold marine sediment under anaerobic and oligotrophic conditions." Canadian Journal of Microbiology 50, no. 2 (February 1, 2004): 91–96. http://dx.doi.org/10.1139/w03-112.
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The in situ degradation of the two nitramine explosives, hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX), was evaluated using a mixture of RDX and HMX, incubated anaerobically at 10 °C with marine sediment from a previous military dumping site of unexploded ordnance (UXO) in Halifax Harbor, Nova Scotia, Canada. The RDX concentration (14.7 mg·L–1) in the aqueous phase was reduced by half in 4 days, while reduction of HMX concentration (1.2 mg·L–1) by half required 50 days. Supplementation with the carbon sources glucose, acetate, or citrate did not affect the removal rate of RDX but improved removal of HMX. Optimal mineralization of RDX and HMX was obtained in the presence of glucose. Using universally labeled (UL)-[14C]RDX, we obtained a carbon mass balance distributed as follows: CO2, 48%–58%; water soluble products, 27%–31%; acetonitrile extractable products, 2.0%–3.4%; and products covalently bound to the sediments and biomass, 8.9% (in the presence of glucose). The disappearance of RDX was accompanied by the formation of the mononitroso derivative hexahydro-1-nitroso-3,5-dinitro-1,3,5-triazine (MNX) and formaldehyde (HCHO) that subsequently disappeared. In the case of HMX, mineralization reached only 13%–27% after 115 days of incubation in the presence or absence of the carbon sources. The disappearance of HMX was also accompanied by the formation of the mononitroso derivative. The total population of psychrotrophic anaerobes that grew at 10 °C was 2.6 × 103 colony-forming units·(g sediment dry mass)–1, and some psychrotrophic sediment isolates were capable of degrading RDX under conditions similar to those used for sediments. Based on the distribution of products, we suggest that the sediment microorganisms degrade RDX and HMX via an initial reduction to the corresponding mononitroso derivative, followed by denitration and ring cleavage.Key words: biodegradation, nitramine explosives, marine sediment, psychrotrophic bacteria.
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Elling, Felix J., Jordon D. Hemingway, Thomas W. Evans, Jenan J. Kharbush, Eva Spieck, Roger E. Summons, and Ann Pearson. "Vitamin B12-dependent biosynthesis ties amplified 2-methylhopanoid production during oceanic anoxic events to nitrification." Proceedings of the National Academy of Sciences 117, no. 52 (December 14, 2020): 32996–3004. http://dx.doi.org/10.1073/pnas.2012357117.
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Bacterial hopanoid lipids are ubiquitous in the geologic record and serve as biomarkers for reconstructing Earth’s climatic and biogeochemical evolution. Specifically, the abundance of 2-methylhopanoids deposited during Mesozoic ocean anoxic events (OAEs) and other intervals has been interpreted to reflect proliferation of nitrogen-fixing marine cyanobacteria. However, there currently is no conclusive evidence for 2-methylhopanoid production by extant marine cyanobacteria. As an alternative explanation, here we report 2-methylhopanoid production by bacteria of the genus Nitrobacter, cosmopolitan nitrite oxidizers that inhabit nutrient-rich freshwater, brackish, and marine environments. The model organism Nitrobacter vulgaris produced only trace amounts of 2-methylhopanoids when grown in minimal medium or with added methionine, the presumed biosynthetic methyl donor. Supplementation of cultures with cobalamin (vitamin B12) increased nitrite oxidation rates and stimulated a 33-fold increase of 2-methylhopanoid abundance, indicating that the biosynthetic reaction mechanism is cobalamin dependent. Because Nitrobacter spp. cannot synthesize cobalamin, we postulate that they acquire it from organisms inhabiting a shared ecological niche—for example, ammonia-oxidizing archaea. We propose that during nutrient-rich conditions, cobalamin-based mutualism intensifies upper water column nitrification, thus promoting 2-methylhopanoid deposition. In contrast, anoxia underlying oligotrophic surface ocean conditions in restricted basins would prompt shoaling of anaerobic ammonium oxidation, leading to low observed 2-methylhopanoid abundances. The first scenario is consistent with hypotheses of enhanced nutrient loading during OAEs, while the second is consistent with the sedimentary record of Pliocene–Pleistocene Mediterranean sapropel events. We thus hypothesize that nitrogen cycling in the Pliocene–Pleistocene Mediterranean resembled modern, highly stratified basins, whereas no modern analog exists for OAEs.
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Rooks, Christine, James Kar-Hei Fang, Pål Tore Mørkved, Rui Zhao, Hans Tore Rapp, Joana R. Xavier, and Friederike Hoffmann. "Deep-sea sponge grounds as nutrient sinks: denitrification is common in boreo-Arctic sponges." Biogeosciences 17, no. 5 (March 6, 2020): 1231–45. http://dx.doi.org/10.5194/bg-17-1231-2020.
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Abstract. Sponges are commonly known as general nutrient providers for the marine ecosystem, recycling organic matter into various forms of bioavailable nutrients such as ammonium and nitrate. In this study we challenge this view. We show that nutrient removal through microbial denitrification is a common feature in six cold-water sponge species from boreal and Arctic sponge grounds. Denitrification rates were quantified by incubating sponge tissue sections with 15NO3--amended oxygen-saturated seawater, mimicking conditions in pumping sponges, and de-oxygenated seawater, mimicking non-pumping sponges. It was not possible to detect any rates of anaerobic ammonium oxidation (anammox) using incubations with 15NH4+. Denitrification rates of the different sponge species ranged from below detection to 97 nmol N cm−3 sponge d−1 under oxic conditions, and from 24 to 279 nmol N cm−3 sponge d−1 under anoxic conditions. A positive relationship between the highest potential rates of denitrification (in the absence of oxygen) and the species-specific abundances of nirS and nirK genes encoding nitrite reductase, a key enzyme for denitrification, suggests that the denitrifying community in these sponge species is active and prepared for denitrification. The lack of a lag phase in the linear accumulation of the 15N-labelled N2 gas in any of our tissue incubations is another indicator for an active community of denitrifiers in the investigated sponge species. Low rates for coupled nitrification–denitrification indicate that also under oxic conditions, the nitrate used to fuel denitrification rates was derived rather from the ambient seawater than from sponge nitrification. The lack of nifH genes encoding nitrogenase, the key enzyme for nitrogen fixation, shows that the nitrogen cycle is not closed in the sponge grounds. The denitrified nitrogen, no matter its origin, is then no longer available as a nutrient for the marine ecosystem. These results suggest a high potential denitrification capacity of deep-sea sponge grounds based on typical sponge biomass on boreal and Arctic sponge grounds, with areal denitrification rates of 0.6 mmol N m−2 d−1 assuming non-pumping sponges and still 0.3 mmol N m−2 d−1 assuming pumping sponges. This is well within the range of denitrification rates of continental shelf sediments. Anthropogenic impact and global change processes affecting the sponge redox state may thus lead to deep-sea sponge grounds changing their role in marine ecosystem from being mainly nutrient sources to becoming mainly nutrient sinks.
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ZHANG Donmgsheng, 张东声, 刘镇盛 LIU Zhensheng, 张海峰 ZHANG Haifeng, 王小谷 WANG Xiaogu, and 王春生 WANG Chunsheng. "Diversity of anaerobic ammonium oxidation bacteria in marine sediments from the Zhoushan islands." Acta Ecologica Sinica 35, no. 19 (2015). http://dx.doi.org/10.5846/stxb201402210303.
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ДУБОВЧУК, С. С., А. Л. ПОНОМАРЕВА, М. С. БАКУНИНА, А. И. ЕСЬКОВА, Р. Б. ШАКИРОВ, А. И. ОБЖИРОВ, and Н. С. ПОЛОНИК. "Biogeochemical role of anaerobic methane oxidation in marine bottom sediments of the Southern Ocean." Вестник ДВО РАН, no. 5(213) (October 28, 2020). http://dx.doi.org/10.37102/08697698.2020.213.5.003.
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Морские донные отложения представляют собой крупнейший резервуар органических веществ на Земле. Биогеохимический цикл метана в воде связывает aнаэробную деструкцию органического вещества с процессами продукции. Этот цикл состоит из образования и окисления метана, в которых участвуют специализированные группы микроорганизмов, играющие важную роль в глобальном цикле органического вещества и газовом режиме океанов. Метанотрофные микроорганизмы окисляют метан как аэробно, так и анаэробно, значительно уменьшая выброс этого парникового газа в атмосферу. Среди акваторий Мирового океана перечисленные процессы менее всего изучены в полярных регионах, несмотря на их важное значение в исследовании потоков парниковых газов, влияющих на глобальные климатические изменения. Перечисленные аспекты требуют усиления исследований и в Южном океане, так как метанотрофные прокариоты играют важную роль в экологии и функционировании высокобиопродуктивных экосистем. Сегодня наше понимание филогенетического разнообразия, возможностей генома и специфических адаптаций к этому в постоянно холодной среде и в анаэробных условиях донных отложений недостаточно. В ходе научной экспедиции РАН на НИС «Академик Мстислав Келдыш» (рейс 79) нами обнаружены аномалии метана до 1000 нл/л в придонном слое толщи вод в районе прол. Брансфилда, а также штаммы термофильных, нефтеокисляющих и метанотрофных микроорганизмов, исследование которых в береговых лабораториях представляет большой интерес. В статье дан обзор актуальности и перспективных направлений исследований по проблеме газотрофных микроорганизмов в Южном океане. Marine bottom sediments are the largest reservoir of organic matter on Earth. The biogeochemical cycle of methane in water links the anaerobic destruction of organic matter with production processes. This cycle consists of the formation and oxidation of methane, which involves specialized groups of microorganisms that play an important role in the global organic matter cycle and the gas regime of the oceans. Methanotrophic microorganisms oxidize methane both aerobically and anaerobically, significantly reducing the release of this greenhouse gas into the atmosphere. Among the world’s oceans, these processes are least studied in polar regions, despite their importance for studying greenhouse gas flows that affect global climate changes. These aspects require increased research in the Southern Ocean, as methanotrophic bacteria play an important role in the ecology and functioning of highly bio-productive ecosystems. To date, our understanding of phylogenetic diversity, genome capabilities and specific adaptations to this in a constantly cold environment and in anaerobic conditions of bottom sediments is limited. During the scientific expedition of the Russian Academy of Sciences aboard the R/V “Academic Mstislav Keldysh”, flight 79, we found anomalies of methane up to 1000 nl/l in the bottom layer of the water column in the area of the Bransfield Strait, as well as strains of thermophilic, oil-oxidizing and methanotrophic bacteria, which analysis in coastal laboratories is of great interest. The article provides an overview of the relevance and perspective directions of research on the problem of gastrophic microorganisms in the Southern Ocean.
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Sinkko, Hanna, Iina Hepolehto, Christina Lyra, Johanna M. Rinta-Kanto, Anna Villnäs, Joanna Norkko, Alf Norkko, and Sari Timonen. "Increasing oxygen deficiency changes rare and moderately abundant bacterial communities in coastal soft sediments." Scientific Reports 9, no. 1 (November 8, 2019). http://dx.doi.org/10.1038/s41598-019-51432-1.
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Abstract Coastal hypoxia is a major environmental problem worldwide. Hypoxia-induced changes in sediment bacterial communities harm marine ecosystems and alter biogeochemical cycles. Nevertheless, the resistance of sediment bacterial communities to hypoxic stress is unknown. We investigated changes in bacterial communities during hypoxic-anoxic disturbance by artificially inducing oxygen deficiency to the seafloor for 0, 3, 7, and 48 days, with subsequent molecular biological analyses. We further investigated relationships between bacterial communities, benthic macrofauna and nutrient effluxes across the sediment-water-interface during hypoxic-anoxic stress, considering differentially abundant operational taxonomic units (OTUs). The composition of the moderately abundant OTUs changed significantly after seven days of oxygen deficiency, while the abundant and rare OTUs first changed after 48 days. High bacterial diversity maintained the resistance of the communities during oxygen deficiency until it dropped after 48 days, likely due to anoxia-induced loss of macrofaunal diversity and bioturbation. Nutrient fluxes, especially ammonium, correlated positively with the moderate and rare OTUs, including potential sulfate reducers. Correlations may reflect bacteria-mediated nutrient effluxes that accelerate eutrophication. The study suggests that even slightly higher bottom-water oxygen concentrations, which could sustain macrofaunal bioturbation, enable bacterial communities to resist large compositional changes and decrease the harmful consequences of hypoxia in marine ecosystems.
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Wallenius, Anna J., Paula Dalcin Martins, Caroline P. Slomp, and Mike S. M. Jetten. "Anthropogenic and Environmental Constraints on the Microbial Methane Cycle in Coastal Sediments." Frontiers in Microbiology 12 (February 18, 2021). http://dx.doi.org/10.3389/fmicb.2021.631621.
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Large amounts of methane, a potent greenhouse gas, are produced in anoxic sediments by methanogenic archaea. Nonetheless, over 90% of the produced methane is oxidized via sulfate-dependent anaerobic oxidation of methane (S-AOM) in the sulfate-methane transition zone (SMTZ) by consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). Coastal systems account for the majority of total marine methane emissions and typically have lower sulfate concentrations, hence S-AOM is less significant. However, alternative electron acceptors such as metal oxides or nitrate could be used for AOM instead of sulfate. The availability of electron acceptors is determined by the redox zonation in the sediment, which may vary due to changes in oxygen availability and the type and rate of organic matter inputs. Additionally, eutrophication and climate change can affect the microbiome, biogeochemical zonation, and methane cycling in coastal sediments. This review summarizes the current knowledge on the processes and microorganisms involved in methane cycling in coastal sediments and the factors influencing methane emissions from these systems. In eutrophic coastal areas, organic matter inputs are a key driver of bottom water hypoxia. Global warming can reduce the solubility of oxygen in surface waters, enhancing water column stratification, increasing primary production, and favoring methanogenesis. ANME are notoriously slow growers and may not be able to effectively oxidize methane upon rapid sedimentation and shoaling of the SMTZ. In such settings, ANME-2d (Methanoperedenaceae) and ANME-2a may couple iron- and/or manganese reduction to AOM, while ANME-2d and NC10 bacteria (Methylomirabilota) could couple AOM to nitrate or nitrite reduction. Ultimately, methane may be oxidized by aerobic methanotrophs in the upper millimeters of the sediment or in the water column. The role of these processes in mitigating methane emissions from eutrophic coastal sediments, including the exact pathways and microorganisms involved, are still underexplored, and factors controlling these processes are unclear. Further studies are needed in order to understand the factors driving methane-cycling pathways and to identify the responsible microorganisms. Integration of the knowledge on microbial pathways and geochemical processes is expected to lead to more accurate predictions of methane emissions from coastal zones in the future.
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Amaral, Valentina, Cristina Romera-Castillo, and Jesús Forja. "Submarine mud volcanoes as a source of chromophoric dissolved organic matter to the deep waters of the Gulf of Cádiz." Scientific Reports 11, no. 1 (February 5, 2021). http://dx.doi.org/10.1038/s41598-021-82632-3.
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AbstractSeafloor structures related to the emission of different fluids, such as submarine mud volcanoes (MVs), have been recently reported to largely contribute with dissolved organic matter (DOM) into the oceans. Submarine MVs are common structures in the Gulf of Cádiz. However, little is known about the biogeochemical processes that occur in these peculiar environments, especially those involving DOM. Here, we report DOM characterization in the sediment pore water of three MVs of the Gulf of Cádiz. Estimated benthic fluxes of dissolved organic carbon (DOC) and chromophoric DOM (CDOM) were higher than in other marine sediments with an average of 0.11 ± 0.04 mmol m−2 d−1 for DOC and ranging between 0.11 and 2.86 m−1 L m−2 d−1, for CDOM. Protein-like components represented ~ 70% of the total fluorescent DOM (FDOM). We found that deep fluids migration from MVs (cold seeps) and anaerobic production via sulfate-reducing bacteria represent a source of DOC and FDOM to the overlying water column. Our results also indicate that fluorescent components can have many diverse sources not captured by common classifications. Overall, MVs act as a source of DOC, CDOM, and FDOM to the deep waters of the Gulf of Cádiz, providing energy to the microbial communities living there.
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Hahn, Cedric Jasper, Rafael Laso-Pérez, Francesca Vulcano, Konstantinos-Marios Vaziourakis, Runar Stokke, Ida Helene Steen, Andreas Teske, et al. "“Candidatus Ethanoperedens,” a Thermophilic Genus of Archaea Mediating the Anaerobic Oxidation of Ethane." mBio 11, no. 2 (April 21, 2020). http://dx.doi.org/10.1128/mbio.00600-20.
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ABSTRACT Cold seeps and hydrothermal vents deliver large amounts of methane and other gaseous alkanes into marine surface sediments. Consortia of archaea and partner bacteria thrive on the oxidation of these alkanes and its coupling to sulfate reduction. The inherently slow growth of the involved organisms and the lack of pure cultures have impeded the understanding of the molecular mechanisms of archaeal alkane degradation. Here, using hydrothermal sediments of the Guaymas Basin (Gulf of California) and ethane as the substrate, we cultured microbial consortia of a novel anaerobic ethane oxidizer, “Candidatus Ethanoperedens thermophilum” (GoM-Arc1 clade), and its partner bacterium “Candidatus Desulfofervidus auxilii,” previously known from methane-oxidizing consortia. The sulfate reduction activity of the culture doubled within one week, indicating a much faster growth than in any other alkane-oxidizing archaea described before. The dominance of a single archaeal phylotype in this culture allowed retrieval of a closed genome of “Ca. Ethanoperedens,” a sister genus of the recently reported ethane oxidizer “Candidatus Argoarchaeum.” The metagenome-assembled genome of “Ca. Ethanoperedens” encoded a complete methanogenesis pathway including a methyl-coenzyme M reductase (MCR) that is highly divergent from those of methanogens and methanotrophs. Combined substrate and metabolite analysis showed ethane as the sole growth substrate and production of ethyl-coenzyme M as the activation product. Stable isotope probing demonstrated that the enzymatic mechanism of ethane oxidation in “Ca. Ethanoperedens” is fully reversible; thus, its enzymatic machinery has potential for the biotechnological development of microbial ethane production from carbon dioxide. IMPORTANCE In the seabed, gaseous alkanes are oxidized by syntrophic microbial consortia that thereby reduce fluxes of these compounds into the water column. Because of the immense quantities of seabed alkane fluxes, these consortia are key catalysts of the global carbon cycle. Due to their obligate syntrophic lifestyle, the physiology of alkane-degrading archaea remains poorly understood. We have now cultivated a thermophilic, relatively fast-growing ethane oxidizer in partnership with a sulfate-reducing bacterium known to aid in methane oxidation and have retrieved the first complete genome of a short-chain alkane-degrading archaeon. This will greatly enhance the understanding of nonmethane alkane activation by noncanonical methyl-coenzyme M reductase enzymes and provide insights into additional metabolic steps and the mechanisms underlying syntrophic partnerships. Ultimately, this knowledge could lead to the biotechnological development of alkanogenic microorganisms to support the carbon neutrality of industrial processes.