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Journal articles on the topic 'Sediment microbial communities'

Author: Grafiati
Published: 10 March 2023

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1

Li, Junwei, Suwen Chen, Peng Wu, et al. "Insights into the Relationship between Intestinal Microbiota of the Aquaculture Worm Sipunculus nudus and Surrounding Sediments." Fishes 8, no. 1 (2023): 32. http://dx.doi.org/10.3390/fishes8010032.

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Sipunculus nudus is an important intertidal aquaculture species that can ingest organic matter from the surface sediment and shows a high transportation capacity in sediment. However, little is known about the influence of intertidal aquaculture species on the sediment microbial community and the exchange of microbiota between the intestine and the surrounding sediment. In this study, the microbial communities in the intestine of S. nudus and three kinds of surrounding sediments were analyzed using high-throughput sequencing of the 16S rRNA gene amplicon, and the relationships between differen
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Oest, Adam, Ali Alsaffar, Mitchell Fenner, Dominic Azzopardi, and Sonia M. Tiquia-Arashiro. "Patterns of Change in Metabolic Capabilities of Sediment Microbial Communities in River and Lake Ecosystems." International Journal of Microbiology 2018 (May 27, 2018): 1–15. http://dx.doi.org/10.1155/2018/6234931.

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Information on the biodegradation potential of lake and river microbial communities is essential for watershed management. The water draining into the lake ecosystems often carries a significant amount of suspended sediments, which are transported by rivers and streams from the local drainage basin. The organic carbon processing in the sediments is executed by heterotrophic microbial communities, whose activities may vary spatially and temporally. Thus, to capture and apprehend some of these variabilities in the sediments, we sampled six sites: three from the Saint Clair River (SC1, SC2, and S
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Rutere, Cyrus, Kirsten Knoop, Malte Posselt, Adrian Ho, and Marcus A. Horn. "Ibuprofen Degradation and Associated Bacterial Communities in Hyporheic Zone Sediments." Microorganisms 8, no. 8 (2020): 1245. http://dx.doi.org/10.3390/microorganisms8081245.

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Ibuprofen, a non-steroidal anti-inflammatory pain reliever, is among pharmaceutical residues of environmental concern ubiquitously detected in wastewater effluents and receiving rivers. Thus, ibuprofen removal potentials and associated bacteria in the hyporheic zone sediments of an impacted river were investigated. Microbially mediated ibuprofen degradation was determined in oxic sediment microcosms amended with ibuprofen (5, 40, 200, and 400 µM), or ibuprofen and acetate, relative to an un-amended control. Ibuprofen was removed by the original sediment microbial community as well as in ibupro
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Wang, Yu, Hua-Fang Sheng, Yan He, et al. "Comparison of the Levels of Bacterial Diversity in Freshwater, Intertidal Wetland, and Marine Sediments by Using Millions of Illumina Tags." Applied and Environmental Microbiology 78, no. 23 (2012): 8264–71. http://dx.doi.org/10.1128/aem.01821-12.

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ABSTRACTSediment, a special realm in aquatic environments, has high microbial diversity. While there are numerous reports about the microbial community in marine sediment, freshwater and intertidal sediment communities have been overlooked. The present study determined millions of Illumina reads for a comparison of bacterial communities in freshwater, intertidal wetland, and marine sediments along Pearl River, China, using a technically consistent approach. Our results show that both taxon richness and evenness were the highest in freshwater sediment, medium in intertidal sediment, and lowest
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Wu, Miao, Ming Zhang, Wei Ding, et al. "Microbial Carbon Metabolic Functions in Sediments Influenced by Resuspension Event." Water 13, no. 1 (2020): 7. http://dx.doi.org/10.3390/w13010007.

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Microorganisms in sediments are an important part of the aquatic ecosystem, and their functional activities are sensitive to external environmental pressure. Shallow lakes are characterized by frequent sediment resuspension events, leading to large amounts of nutrients being released. However, information about the potential impacts of sediment resuspension events on the functional activities of microbial communities is limited. In this study, the responses of microbial carbon metabolism in sediments under different wind–wave disturbance were analyzed by BIOLOG ECO microplates. The results sho
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Kuo, Jimmy, Daniel Liu, and Chorng-Horng Lin. "Functional Prediction of Microbial Communities in Sediment Microbial Fuel Cells." Bioengineering 10, no. 2 (2023): 199. http://dx.doi.org/10.3390/bioengineering10020199.

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Sediment microbial fuel cells (MFCs) were developed in which the complex substrates present in the sediment could be oxidized by microbes for electron production. In this study, the functional prediction of microbial communities of anode-associated soils in sediment MFCs was investigated based on 16S rRNA genes. Four computational approaches, including BugBase, Functional Annotation of Prokaryotic Taxa (FAPROTAX), the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2), and Tax4Fun2, were applied. A total of 67, 9, 37, and 38 functional features were sta
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7

Laverock, Bonnie, Jack A. Gilbert, Karen Tait, A. Mark Osborn, and Steve Widdicombe. "Bioturbation: impact on the marine nitrogen cycle." Biochemical Society Transactions 39, no. 1 (2011): 315–20. http://dx.doi.org/10.1042/bst0390315.

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Sediments play a key role in the marine nitrogen cycle and can act either as a source or a sink of biologically available (fixed) nitrogen. This cycling is driven by a number of microbial remineralization reactions, many of which occur across the oxic/anoxic interface near the sediment surface. The presence and activity of large burrowing macrofauna (bioturbators) in the sediment can significantly affect these microbial processes by altering the physicochemical properties of the sediment. For example, the building and irrigation of burrows by bioturbators introduces fresh oxygenated water into
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8

Hölker, Franz, Christian Wurzbacher, Carsten Weißenborn, Michael T. Monaghan, Stephanie I. J. Holzhauer, and Katrin Premke. "Microbial diversity and community respiration in freshwater sediments influenced by artificial light at night." Philosophical Transactions of the Royal Society B: Biological Sciences 370, no. 1667 (2015): 20140130. http://dx.doi.org/10.1098/rstb.2014.0130.

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An increasing proportion of the Earth's surface is illuminated at night. In aquatic ecosystems, artificial light at night (ALAN) may influence microbial communities living in the sediments. These communities are highly diverse and play an important role in the global carbon cycle. We combined field and laboratory experiments using sediments from an agricultural drainage system to examine how ALAN affects communities and alters carbon mineralization. Two identical light infrastructures were installed parallel to a drainage ditch before the start of the experiment. DNA metabarcoding indicated th
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Marfil-Santana, Miguel David, Anahí Martínez-Cárdenas, Analuisa Ruíz-Hernández, et al. "A Meta-Omics Analysis Unveils the Shift in Microbial Community Structures and Metabolomics Profiles in Mangrove Sediments Treated with a Selective Actinobacterial Isolation Procedure." Molecules 26, no. 23 (2021): 7332. http://dx.doi.org/10.3390/molecules26237332.

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Mangrove sediment ecosystems in the coastal areas of the Yucatan peninsula are unique environments, influenced by their karstic origin and connection with the world’s largest underground river. The microbial communities residing in these sediments are influenced by the presence of mangrove roots and the trading chemistry for communication between sediment bacteria and plant roots can be targeted for secondary metabolite research. To explore the secondary metabolite production potential of microbial community members in mangrove sediments at the “El Palmar” natural reserve in Sisal, Yucatan, a
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Tufail, Azra. "Microbial communities colonising nutrient-enriched marine sediment." Hydrobiologia 148, no. 3 (1987): 245–55. http://dx.doi.org/10.1007/bf00017527.

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Yang, Yuyin, Ningning Li, Wei Wang, Bingxin Li, Shuguang Xie, and Yong Liu. "Vertical profiles of sediment methanogenic potential and communities in two plateau freshwater lakes." Biogeosciences 14, no. 2 (2017): 341–51. http://dx.doi.org/10.5194/bg-14-341-2017.

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Abstract. Microbial methanogenesis in sediment plays a crucial role in CH4 emission from freshwater lake ecosystems. However, knowledge of the layer-depth-related changes of methanogen community structure and activities in freshwater lake sediment is still limited. The present study was conducted to characterize the methanogenesis potential in different sediment-layer depths and the vertical distribution of microbial communities in two freshwater lakes of different trophic status on the Yunnan Plateau (China). Incubation experiments and inhibitor studies were carried out to determine the metha
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Elmer, Wade H., Peter Thiel, and Blaire Steven. "Response of Sediment Bacterial Communities to Sudden Vegetation Dieback in a Coastal Wetland." Phytobiomes Journal 1, no. 1 (2017): 5–13. http://dx.doi.org/10.1094/pbiomes-09-16-0006-r.

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There is an increasing recognition of the role coastal vegetated ecosystems play in atmospheric carbon sequestration. However, the development of sudden vegetation dieback (SVD), a phenomenon that causes the rapid death of Spartina alterniflora, followed by no or slow recovery, has affected large-scale alterations in Atlantic coastal systems. This study reports the effects of the development of SVD on the sediment microbial communities. In 1999, Hammonasset Beach State Park in Connecticut experienced the initial appearance of SVD. After more than a decade, the plants have not recovered. Yet, s
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Wyness, Adam J., Irene Fortune, Andrew J. Blight, et al. "Ecosystem engineers drive differing microbial community composition in intertidal estuarine sediments." PLOS ONE 16, no. 2 (2021): e0240952. http://dx.doi.org/10.1371/journal.pone.0240952.

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Intertidal systems are complex and dynamic environments with many interacting factors influencing biochemical characteristics and microbial communities. One key factor are the actions of resident fauna, many of which are regarded as ecosystem engineers because of their bioturbation, bioirrigation and sediment stabilising activities. The purpose of this investigation was to elucidate the evolutionary implications of the ecosystem engineering process by identifying, if any, aspects that act as selection pressures upon microbial communities. A mesocosm study was performed using the well character
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Boulding, A. N., G. N. Rees, D. S. Baldwin, P. J. Suter, and G. O. Watson. "Changes in sediment microbial community structure within a large water-storage reservoir during an extreme drawdown event." Marine and Freshwater Research 59, no. 10 (2008): 890. http://dx.doi.org/10.1071/mf07232.

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Although drought and drying of waters occur globally, the effect of drying on sediment microbial communities underpinning aquatic biogeochemical processes is poorly understood. We used the molecular method of terminal-restriction fragment length polymorphism (T-RFLP) to assess changes in the microbial community structure of sediments undergoing different levels of inundation and drying within a reservoir during drawdown in a drought. Sediments with three hydrological conditions were investigated: dry sediments (no overlying water), littoral sediments (covered with 1–2 mm water) and inundated s
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15

Weisbrod, Barbara, Susanna A. Wood, Konstanze Steiner, et al. "Is a Central Sediment Sample Sufficient? Exploring Spatial and Temporal Microbial Diversity in a Small Lake." Toxins 12, no. 9 (2020): 580. http://dx.doi.org/10.3390/toxins12090580.

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(1) Background: Paleolimnological studies use sediment cores to explore long-term changes in lake ecology, including occurrences of harmful cyanobacterial blooms. Most studies are based on single cores, assuming this is representative of the whole lake, but data on small-scale spatial variability of microbial communities in lake sediment are scarce. (2) Methods: Surface sediments (top 0.5 cm) from 12 sites (n = 36) and two sediment cores were collected in Lake Rotorua (New Zealand). Bacterial community (16S rRNA metabarcoding), Microcystis specific 16S rRNA, microcystin synthetase gene E (mcyE
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Ramírez, Gustavo A., Paraskevi Mara, Taylor Sehein, et al. "Environmental factors shaping bacterial, archaeal and fungal community structure in hydrothermal sediments of Guaymas Basin, Gulf of California." PLOS ONE 16, no. 9 (2021): e0256321. http://dx.doi.org/10.1371/journal.pone.0256321.

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The flanking regions of Guaymas Basin, a young marginal rift basin located in the Gulf of California, are covered with thick sediment layers that are hydrothermally altered due to magmatic intrusions. To explore environmental controls on microbial community structure in this complex environment, we analyzed site- and depth-related patterns of microbial community composition (bacteria, archaea, and fungi) in hydrothermally influenced sediments with different thermal conditions, geochemical regimes, and extent of microbial mats. We compared communities in hot hydrothermal sediments (75-100°C at
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Hoshino, Tatsuhiko, Hideyuki Doi, Go-Ichiro Uramoto, et al. "Global diversity of microbial communities in marine sediment." Proceedings of the National Academy of Sciences 117, no. 44 (2020): 27587–97. http://dx.doi.org/10.1073/pnas.1919139117.

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Microbial life in marine sediment contributes substantially to global biomass and is a crucial component of the Earth system. Subseafloor sediment includes both aerobic and anaerobic microbial ecosystems, which persist on very low fluxes of bioavailable energy over geologic time. However, the taxonomic diversity of the marine sedimentary microbial biome and the spatial distribution of that diversity have been poorly constrained on a global scale. We investigated 299 globally distributed sediment core samples from 40 different sites at depths of 0.1 to 678 m below the seafloor. We obtained ∼47
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18

Fiskal, Annika, Aixala Gaillard, Sebastien Giroud, et al. "Effects of Macrofaunal Recolonization on Biogeochemical Processes and Microbiota—A Mesocosm Study." Water 13, no. 11 (2021): 1599. http://dx.doi.org/10.3390/w13111599.

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Macroinvertebrates are widespread in lake sediments and alter sedimentary properties through their activity (bioturbation). Understanding the interactions between bioturbation and sediment properties is important given that lakes are important sinks and sources of carbon and nutrients. We studied the biogeochemical impact of macrofauna on surface sediments in 3-month-long mesocosm experiments conducted using sediment cores from a hypoxic, macrofauna-free lake basin. Experimental units consisted of hypoxic controls, oxic treatments, and oxic treatments that were experimentally colonized with ch
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19

Pop Ristova, P., F. Wenzhöfer, A. Ramette, et al. "Bacterial diversity and biogeochemistry of different chemosynthetic habitats of the REGAB cold seep (West African margin, 3160 m water depth)." Biogeosciences Discussions 9, no. 7 (2012): 8337–85. http://dx.doi.org/10.5194/bgd-9-8337-2012.

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Abstract. The giant pockmark REGAB (West African margin, 3160 m water depth) is an active methane-emitting cold seep ecosystem, where the energy derived from microbially mediated oxidation of methane supports high biomass and diversity of chemosynthetic communities. Bare sediments interspersed with heterogeneous chemosynthetic assemblages of mytilid mussels, vesicomyid clams and siboglinid tubeworms form a complex seep ecosystem. To better understand if benthic bacterial communities reflect the patchy distribution of chemosynthetic fauna, all major chemosynthetic habitats at REGAB were investi
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Pop Ristova, P., F. Wenzhöfer, A. Ramette, et al. "Bacterial diversity and biogeochemistry of different chemosynthetic habitats of the REGAB cold seep (West African margin, 3160 m water depth)." Biogeosciences 9, no. 12 (2012): 5031–48. http://dx.doi.org/10.5194/bg-9-5031-2012.

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Abstract. The giant pockmark REGAB (West African margin, 3160 m water depth) is an active methane-emitting cold seep ecosystem, where the energy derived from microbially mediated oxidation of methane supports high biomass and diversity of chemosynthetic communities. Bare sediments interspersed with heterogeneous chemosynthetic assemblages of mytilid mussels, vesicomyid clams and siboglinid tubeworms form a complex seep ecosystem. To better understand if benthic bacterial communities reflect the patchy distribution of chemosynthetic fauna, all major chemosynthetic habitats at REGAB were investi
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Kawamoto, Yasutake, Hiromi Kato, Yuji Nagata, and Jotaro Urabe. "Microbial communities developing within bulk sediments under fish carcasses on a tidal flat." PLOS ONE 16, no. 2 (2021): e0247220. http://dx.doi.org/10.1371/journal.pone.0247220.

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Animal carcasses are often brought into tidal flats where they are at the boundary between terrestrial and marine ecosystems. Since these carcasses act as microhabitats with large amounts of energy and nutrients, they likely develop unique bacterial assemblages in the ambient sediment, which in turn may stimulate colonization of other organisms such as protozoans. However, little is known about the microbial assemblages colonized in sediment around animal carcasses in the tidal zone. Herein we examined the bacterial and ciliophoran assemblages developed in association with fish carcasses by in
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Noble, Peter A., Jonas S. Almeida, and Charles R. Lovell. "Application of Neural Computing Methods for Interpreting Phospholipid Fatty Acid Profiles of Natural Microbial Communities." Applied and Environmental Microbiology 66, no. 2 (2000): 694–99. http://dx.doi.org/10.1128/aem.66.2.694-699.2000.

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ABSTRACT The microbial community compositions of surface and subsurface marine sediments and sediments lining burrows of marine polychaetes and hemichordates from the North Inlet estuary (near Georgetown, S.C.) were analyzed by comparing ester-linked phospholipid fatty acid (PLFA) profiles with a back-propagating neural network (NN). The NNs were trained to relate PLFA inputs to sediment type outputs (e.g., surface, subsurface, and burrow lining) and worm species (e.g., Notomastus lobatus, Balanoglossus aurantiacus, andBranchyoasychus americana). Sensitivity analysis was used to determine whic
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Ettinger, Cassandra L., Susan L. Williams, Jessica M. Abbott, John J. Stachowicz, and Jonathan A. Eisen. "Microbiome succession during ammonification in eelgrass bed sediments." PeerJ 5 (August 16, 2017): e3674. http://dx.doi.org/10.7717/peerj.3674.

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BackgroundEelgrass (Zostera marina) is a marine angiosperm and foundation species that plays an important ecological role in primary production, food web support, and elemental cycling in coastal ecosystems. As with other plants, the microbial communities living in, on, and near eelgrass are thought to be intimately connected to the ecology and biology of eelgrass. Here we characterized the microbial communities in eelgrass sediments throughout an experiment to quantify the rate of ammonification, the first step in early remineralization of organic matter, also known as diagenesis, from plots
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Navarrete-Euan, Herón, Zuemy Rodríguez-Escamilla, Ernesto Pérez-Rueda, Karla Escalante-Herrera, and Mario Alberto Martínez-Núñez. "Comparing Sediment Microbiomes in Contaminated and Pristine Wetlands along the Coast of Yucatan." Microorganisms 9, no. 4 (2021): 877. http://dx.doi.org/10.3390/microorganisms9040877.

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Microbial communities are important players in coastal sediments for the functioning of the ecosystem and the regulation of biogeochemical cycles. They also have great potential as indicators of environmental perturbations. To assess how microbial communities can change their composition and abundance along coastal areas, we analyzed the composition of the microbiome of four locations of the Yucatan Peninsula using 16S rRNA gene amplicon sequencing. To this end, sediment from two conserved (El Palmar and Bocas de Dzilam) and two contaminated locations (Sisal and Progreso) from the coast northw
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Frischer, Marc E., Jean M. Danforth, Michele A. Newton Healy, and F. Michael Saunders. "Whole-Cell versus Total RNA Extraction for Analysis of Microbial Community Structure with 16S rRNA-Targeted Oligonucleotide Probes in Salt Marsh Sediments." Applied and Environmental Microbiology 66, no. 7 (2000): 3037–43. http://dx.doi.org/10.1128/aem.66.7.3037-3043.2000.

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ABSTRACT rRNA-targeted oligonucleotide probes have become powerful tools for describing microbial communities, but their use in sediments remains difficult. Here we describe a simple technique involving homogenization, detergents, and dispersants that allows the quantitative extraction of cells from formalin-preserved salt marsh sediments. Resulting cell extracts are amenable to membrane blotting and hybridization protocols. Using this procedure, the efficiency of cell extraction was high (95.7% � 3.7% [mean � standard deviation]) relative to direct DAPI (4′,6′-diamidino-2-phenylindo
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Hullar, Meredith A. J., Louis A. Kaplan, and David A. Stahl. "Recurring Seasonal Dynamics of Microbial Communities in Stream Habitats." Applied and Environmental Microbiology 72, no. 1 (2006): 713–22. http://dx.doi.org/10.1128/aem.72.1.713-722.2006.

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ABSTRACT Recurring seasonal patterns of microbial distribution and abundance in three third-order temperate streams within the southeast Pennsylvania Piedmont were observed over 4 years. Populations associated with streambed sediments and rocks (epilithon) were identified using terminal restriction length polymorphism (tRFLP) and sequencing of 16S rRNA genes selectively amplified with primers for the bacterial domain. Analyses of the relative magnitudes of tRFLP peak areas by using nonmetric multidimensional scaling resolved clear seasonal trends in epilithic and sediment populations. Oscillat
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Kurtz, Janis C., Richard Devereux, Tamar Barkay, and Robert B. Jonas. "Evaluation of sediment slurry microcosms for modeling microbial communities in estuarine sediments." Environmental Toxicology and Chemistry 17, no. 7 (1998): 1274–81. http://dx.doi.org/10.1002/etc.5620170712.

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Matsui, George Y., David B. Ringelberg, and Charles R. Lovell. "Sulfate-Reducing Bacteria in Tubes Constructed by the Marine Infaunal Polychaete Diopatra cuprea." Applied and Environmental Microbiology 70, no. 12 (2004): 7053–65. http://dx.doi.org/10.1128/aem.70.12.7053-7065.2004.

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ABSTRACT Marine infaunal burrows and tubes greatly enhance solute transport between sediments and the overlying water column and are sites of elevated microbial activity. Biotic and abiotic controls of the compositions and activities of burrow and tube microbial communities are poorly understood. The microbial communities in tubes of the marine infaunal polychaete Diopatria cuprea collected from two different sediment habitats were examined. The bacterial communities in the tubes from a sandy sediment differed from those in the tubes from a muddy sediment. The difference in community structure
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Liu, Qian, Junnan Li, Hongwei Shan, and Yicheng Xie. "Metagenomic Insights into the Structure of Microbial Communities Involved in Nitrogen Cycling in Two Integrated Multitrophic Aquaculture (IMTA) Ponds." Journal of Marine Science and Engineering 10, no. 2 (2022): 171. http://dx.doi.org/10.3390/jmse10020171.

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The microbial structure and metabolic potential, particularly with regard to nitrogen (N) cycling, in integrated multitrophic aquaculture (IMTA) ponds with shrimp remain unclear. In this study, an analysis of microbial community taxonomic diversity and a metagenomic analysis of N-related genes were performed in a shrimp-crab pond (Penaeus japonicus-Portunus trituberculatus, SC) and a shrimp-crab-clam pond (P. japonicus-P. trituberculatus-Sinonovacula constricta, SCC) to evaluate microbial structure and N transformation capacities in these two shrimp IMTA ponds. The composition of the microbial
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Federle, Thomas W., Robert J. Livingston, Loretta E. Wolfe, and David C. White. "A quantitative comparison of microbial community structure of estuarine sediments from microcosms and the field." Canadian Journal of Microbiology 32, no. 4 (1986): 319–25. http://dx.doi.org/10.1139/m86-063.

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Estuarine soft-bottom sediments in microcosms and the field were compared with regard to microbial community structure. Community structure was determined by analyzing the fatty acids derived from the microbial lipids in the sediments. Fatty acid profiles were compared using a multivariate statistical approach. Experiments were performed using sediments from St. George Sound and Apalachicola Bay, Florida. The community structure of St. George Sound sediments was apparently controlled by epibenthic predators. In Apalachicola Bay, the dominant influences were physical factors related to the flow
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Angermeyer, Angus, Sarah C. Crosby, and Julie A. Huber. "Salt marsh sediment bacterial communities maintain original population structure after transplantation across a latitudinal gradient." PeerJ 6 (May 1, 2018): e4735. http://dx.doi.org/10.7717/peerj.4735.

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Dispersal and environmental selection are two of the most important factors that govern the distributions of microbial communities in nature. While dispersal rates are often inferred by measuring the degree to which community similarity diminishes with increasing geographic distance, determining the extent to which environmental selection impacts the distribution of microbes is more complex. To address this knowledge gap, we performed a large reciprocal transplant experiment to simulate the dispersal of US East Coast salt marsh Spartina alterniflora rhizome-associated microbial sediment commun
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Weingarten, Eric A., Lauren A. Lawson, and Colin R. Jackson. "The Saltpan Microbiome Is Structured by Sediment Depth and Minimally Influenced by Variable Hydration." Microorganisms 8, no. 4 (2020): 538. http://dx.doi.org/10.3390/microorganisms8040538.

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Saltpans are a class of ephemeral wetland characterized by alternating periods of inundation, rising salinity, and desiccation. We obtained soil cores from a saltpan on the Mississippi Gulf coast in both the inundated and desiccated state. The microbiomes of surface and 30 cm deep sediment were determined using Illumina sequencing of the V4 region of the 16S rRNA gene. Bacterial and archaeal community composition differed significantly between sediment depths but did not differ between inundated and desiccated states. Well-represented taxa included marine microorganisms as well as multiple hal
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Reed, David W., Yoshiko Fujita, Mark E. Delwiche, et al. "Microbial Communities from Methane Hydrate-Bearing Deep Marine Sediments in a Forearc Basin." Applied and Environmental Microbiology 68, no. 8 (2002): 3759–70. http://dx.doi.org/10.1128/aem.68.8.3759-3770.2002.

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ABSTRACT Microbial communities in cores obtained from methane hydrate-bearing deep marine sediments (down to more than 300 m below the seafloor) in the forearc basin of the Nankai Trough near Japan were characterized with cultivation-dependent and -independent techniques. Acridine orange direct count data indicated that cell numbers generally decreased with sediment depth. Lipid biomarker analyses indicated the presence of viable biomass at concentrations greater than previously reported for terrestrial subsurface environments at similar depths. Archaeal lipids were more abundant than bacteria
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Bi, Sheng, Han Lai, Dingli Guo, et al. "The Characteristics of Intestinal Bacterial Community in Three Omnivorous Fishes and Their Interaction with Microbiota from Habitats." Microorganisms 9, no. 10 (2021): 2125. http://dx.doi.org/10.3390/microorganisms9102125.

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Artificial fishery habitats have been extensively used for fishery resource protection and water habitat restoration, and they could attract a large number of omnivorous fishes to gather together. This study intended to reveal the relationship between bacterial communities in the habitats (water and sediment) and intestines of omnivorous fishes (Oreochromis mossambicus, Toxabramis houdemeri and Hemiculter leucisculus). Therefore, we investigated the bacterial communities of samples collected from intestines, water, and sediments in artificial fishery habitats via 16S rRNA metabarcoding high-th
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Pham, Huynh A., Carolyn E. Oldham, and Jason J. Plumb. "The Diversity of Benthic Microorganisms in Acidic Mine Lake Sediments." Advanced Materials Research 20-21 (July 2007): 489–92. http://dx.doi.org/10.4028/www.scientific.net/amr.20-21.489.

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The sediment microbial communities of a disused coal mine lake, Lake Kepwari (pH~4.5-5) were studied to understand how the natural microbial processes in an oligotrophic acidic mine lake system influence the iron and sulphur cycles. Most probable number (MPN) viable counts were used to enumerate the benthic bacteria at different depths. MPN results revealed an abundance of bacteria that were capable of growing in sulphate reducing medium with numbers in the range of 1 × 107 – 1 × 108 cells.g-1 of wet sediment. In contrast, MPN results showed much lower numbers of bacteria that were capable of
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Teske, A., A. Durbin, K. Ziervogel, C. Cox, and C. Arnosti. "Microbial Community Composition and Function in Permanently Cold Seawater and Sediments from an Arctic Fjord of Svalbard." Applied and Environmental Microbiology 77, no. 6 (2011): 2008–18. http://dx.doi.org/10.1128/aem.01507-10.

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ABSTRACTHeterotrophic microbial communities in seawater and sediments metabolize much of the organic carbon produced in the ocean. Although carbon cycling and preservation depend critically on the capabilities of these microbial communities, their compositions and capabilities have seldom been examined simultaneously at the same site. To compare the abilities of seawater and sedimentary microbial communities to initiate organic matter degradation, we measured the extracellular enzymatic hydrolysis rates of 10 substrates (polysaccharides and algal extracts) in surface seawater and bottom water
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Lozupone, Catherine, and Rob Knight. "UniFrac: a New Phylogenetic Method for Comparing Microbial Communities." Applied and Environmental Microbiology 71, no. 12 (2005): 8228–35. http://dx.doi.org/10.1128/aem.71.12.8228-8235.2005.

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ABSTRACT We introduce here a new method for computing differences between microbial communities based on phylogenetic information. This method, UniFrac, measures the phylogenetic distance between sets of taxa in a phylogenetic tree as the fraction of the branch length of the tree that leads to descendants from either one environment or the other, but not both. UniFrac can be used to determine whether communities are significantly different, to compare many communities simultaneously using clustering and ordination techniques, and to measure the relative contributions of different factors, such
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Neff, Alexis N., Dean M. DeNicola, and Chris Maltman. "Passive Treatment for Acid Mine Drainage Partially Restores Microbial Community Structure in Different Stream Habitats." Water 13, no. 22 (2021): 3300. http://dx.doi.org/10.3390/w13223300.

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The assessment of the degree to which biological communities in streams impaired by acid mine drainage (AMD) are restored by passive treatment has focused primarily on eukaryotic-cell organisms and microbial processes. The responses of microbial community structure to passive treatment have received much less attention, even though functional processes such as nutrient cycling and organic matter decomposition depend on taxonomic composition. Our objective was to determine the degree to which passive treatment restored microbial communities in three types of habitats: aqueous, leaf, and sedimen
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Cui, Guojie, Jun Li, Zhaoming Gao, and Yong Wang. "Spatial variations of microbial communities in abyssal and hadal sediments across the Challenger Deep." PeerJ 7 (May 17, 2019): e6961. http://dx.doi.org/10.7717/peerj.6961.

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Microbial communities in hadal sediments are least explored in hadal zone (>6,000 m), especially in the Challenger Deep with high pressure (∼110 M pa at the bottom). In this study, we investigated the microbial communities in the sediments of the slope and trench-axis bottom of the Challenger Deep in the Mariana Trench. Classification of the reads of the 16S rRNA gene amplicons showed vertical distribution of prokaryotic microbial inhabitants from the surface to up to 60 centimeter below surface floor (cmbsf). The most dominant phyla were Proteobacteria, Chloroflexi, Actinobacteria, Plancto
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Sauer, Hailey M., Trinity L. Hamilton, Rika E. Anderson, Charles E. Umbanhowar, and Adam J. Heathcote. "Diversity and distribution of sediment bacteria across an ecological and trophic gradient." PLOS ONE 17, no. 3 (2022): e0258079. http://dx.doi.org/10.1371/journal.pone.0258079.

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The microbial communities of lake sediments have the potential to serve as valuable bioindicators and integrators of watershed land-use and water quality; however, the relative sensitivity of these communities to physio-chemical and geographical parameters must be demonstrated at taxonomic resolutions that are feasible by current sequencing and bioinformatic approaches. The geologically diverse and lake-rich state of Minnesota (USA) is uniquely situated to address this potential because of its variability in ecological region, lake type, and watershed land-use. In this study, we selected twent
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Thureborn, Petter, Andrea Franzetti, Daniel Lundin, and Sara Sjöling. "Reconstructing ecosystem functions of the active microbial community of the Baltic Sea oxygen depleted sediments." PeerJ 4 (January 19, 2016): e1593. http://dx.doi.org/10.7717/peerj.1593.

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Baltic Sea deep water and sediments hold one of the largest anthropogenically induced hypoxic areas in the world. High nutrient input and low water exchange result in eutrophication and oxygen depletion below the halocline. As a consequence at Landsort Deep, the deepest point of the Baltic Sea, anoxia in the sediments has been a persistent condition over the past decades. Given that microbial communities are drivers of essential ecosystem functions we investigated the microbial community metabolisms and functions of oxygen depleted Landsort Deep sediments by metatranscriptomics. Results show s
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Yasir, Muhammad, Arooj K. Qureshi, and Esam I. Azhar. "16S amplicon sequencing of microbial communities in enriched and non-enriched sediments of non-volcanic hot spring with temperature gradients." PeerJ 9 (April 2, 2021): e10995. http://dx.doi.org/10.7717/peerj.10995.

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Microorganisms in geothermal springs can offer insights into the fundamental and applied study of extremophiles. However, low microbial abundance and culturing requirements limit the ability to analyze microbial diversity in these ecosystems. In this study, culture-dependent and culture-independent techniques were used to analyze sediment samples from the non-volcanic Tatta Pani hot springs in district Poonch of Azad Kashmir. Microbial composition, temperature gradient, and enrichment effects on rare taxa were evaluated. In total, 31 distinct bacterial phyla and 725 genera were identified from
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43

Yang, Chu-Wen, Yi-En Chen, and Bea-Ven Chang. "Microbial Communities Associated with Acetaminophen Biodegradation from Mangrove Sediment." Sustainability 12, no. 13 (2020): 5410. http://dx.doi.org/10.3390/su12135410.

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Acetaminophen (ACE) is a widely used medicine. Currently, concerns regarding its potential adverse effects on the environments are raised. The aim of this study was to evaluate ACE biodegradation in mangrove sediments under aerobic and anaerobic conditions. Three ACE biodegradation strategies in mangrove sediments were tested. The degradation half-lives (t1/2) of ACE in the sediments with spent mushroom compost under aerobic conditions ranged from 3.24 ± 0.16 to 6.25 ± 0.31 d. The degradation half-lives (t1/2) of ACE in sediments with isolated bacterial strains ranged from 2.54 ± 0.13 to 3.30
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Zhang, Zhimin, Qinghui Deng, Lingling Wan, Xiuyun Cao, Yiyong Zhou, and Chunlei Song. "Bacterial Communities and Enzymatic Activities in Sediments of Long-Term Fish and Crab Aquaculture Ponds." Microorganisms 9, no. 3 (2021): 501. http://dx.doi.org/10.3390/microorganisms9030501.

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Aquaculture is among the most important and fastest growing agriculture sectors worldwide; however, it generates environmental impacts by introducing nutrient accumulations in ponds, which are possibly different and further result in complex biological processes in the sediments based on diverse farming practices. In this study, we investigated the effects of long-term farming practices of representative aquatic animals dominated by grass carp (GC, Ctenopharyngodon idella) or Chinese mitten crab (CMC, Eriocheir sinensis) on the bacterial community and enzyme activity of sediments from more tha
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Zeng, Jin, Liu-Yan Yang, Yi Liang, et al. "Spatial distribution of bacterial communities in sediment of a eutrophic lake revealed by denaturing gradient gel electrophoresis and multivariate analysis." Canadian Journal of Microbiology 54, no. 12 (2008): 1053–63. http://dx.doi.org/10.1139/w08-098.

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Bacterial community structure and the effects of several environmental factors on the microbial community distribution were investigated in the sediment of the eutrophic Lake Xuanwu. Profiles of bacterial communities were generated using denaturing gradient gel electrophoresis (DGGE), and the results were interpreted with multivariate statistical analysis. Five major variables in sediment were examined in a principal component analysis, which indicates notable differences of physicochemical parameters among different sites of the lake. To assess changes in the genetic diversity of bacterial co
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Gault, A. G., F. S. Islam, D. A. Polya, et al. "Microcosm depth profiles of arsenic release in a shallow aquifer, West Bengal." Mineralogical Magazine 69, no. 5 (2005): 855–63. http://dx.doi.org/10.1180/0026461056950293.

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AbstractArsenic mobilization and Fe(III) reduction in acetate-amended sediments collected from a range of depths from an aquifer with elevated groundwater arsenic concentrations in West Bengal were monitored over a 1 month period. Significant arsenic release was noted in sediment collected from 24 m and 45 m depth, with some Fe(III) reduction also observed in the 24 m sample. The structure of the microbial communities present in the sediments prior to incubation showed marked differences down the sediment column. Profiling of the microbial community in the 24 m and 45 m samples revealed a rela
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De Schamphelaire, Liesje, Angela Cabezas, Massimo Marzorati, Michael W. Friedrich, Nico Boon, and Willy Verstraete. "Microbial Community Analysis of Anodes from Sediment Microbial Fuel Cells Powered by Rhizodeposits of Living Rice Plants." Applied and Environmental Microbiology 76, no. 6 (2010): 2002–8. http://dx.doi.org/10.1128/aem.02432-09.

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ABSTRACT By placing the anode of a sediment microbial fuel cell (SMFC) in the rhizosphere of a rice plant, root-excreted rhizodeposits can be microbially oxidized with concomitant current generation. Here, various molecular techniques were used to characterize the composition of bacterial and archaeal communities on such anodes, as influenced by electrical circuitry, sediment matrix, and the presence of plants. Closed-circuit anodes in potting soil were enriched with Desulfobulbus-like species, members of the family Geobacteraceae, and as yet uncultured representatives of the domain Archaea.
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North, Nadia N., Sherry L. Dollhopf, Lainie Petrie, Jonathan D. Istok, David L. Balkwill, and Joel E. Kostka. "Change in Bacterial Community Structure during In Situ Biostimulation of Subsurface Sediment Cocontaminated with Uranium and Nitrate." Applied and Environmental Microbiology 70, no. 8 (2004): 4911–20. http://dx.doi.org/10.1128/aem.70.8.4911-4920.2004.

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ABSTRACT Previous studies have demonstrated that metal-reducing microorganisms can effectively promote the precipitation and removal of uranium from contaminated groundwater. Microbial communities were stimulated in the acidic subsurface by pH neutralization and addition of an electron donor to wells. In single-well push-pull tests at a number of treated sites, nitrate, Fe(III), and uranium were extensively reduced and electron donors (glucose, ethanol) were consumed. Examination of sediment chemistry in cores sampled immediately adjacent to treated wells 3.5 months after treatment revealed th
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Mosher, Jennifer J., Robert H. Findlay, and Carl G. Johnston. "Physical and chemical factors affecting microbial biomass and activity in contaminated subsurface riverine sediments." Canadian Journal of Microbiology 52, no. 5 (2006): 397–403. http://dx.doi.org/10.1139/w05-144.

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Over 80 years of direct discharge of industrial effluents into the Mahoning River, located in northeastern Ohio, USA, has led to the accumulation of a wide variety of pollutants within its sediments. This study examined the physical and chemical parameters, including lipophilic pollutants, affecting microbial activity and biomass in subsurface (10–40 cm horizon) sediments. Microbial biomass was higher in anthropogenically contaminated sediments, and step-wise linear regression showed that approximately 82% of the variation in microbial biomass could be explained by total hexane extractable hyd
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Starnawski, Piotr, Thomas Bataillon, Thijs J. G. Ettema, et al. "Microbial community assembly and evolution in subseafloor sediment." Proceedings of the National Academy of Sciences 114, no. 11 (2017): 2940–45. http://dx.doi.org/10.1073/pnas.1614190114.

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Bacterial and archaeal communities inhabiting the subsurface seabed live under strong energy limitation and have growth rates that are orders of magnitude slower than laboratory-grown cultures. It is not understood how subsurface microbial communities are assembled and whether populations undergo adaptive evolution or accumulate mutations as a result of impaired DNA repair under such energy-limited conditions. Here we use amplicon sequencing to explore changes of microbial communities during burial and isolation from the surface to the >5,000-y-old subsurface of marine sediment and identify
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