Journal articles: 'Environmental marine biotechnology'

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Pomponi, Shirley A., Daniel G. Baden, and Yonathan Zohar. "Marine Biotechnology: Realizing the Potential." Marine Technology Society Journal 41, no. 3 (September 1, 2007): 24–31. http://dx.doi.org/10.4031/002533207787442132.

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Marine biotechnology is an applied science, the goal of which is to develop goods and services from marine organisms and processes. The new wave of marine biotechnology research began in the early 1980s and includes some significant success stories. A new drug to manage pain is commercially available, and a new cancer drug has been recommended for approval, the first from a fish-eating snail and the second from a mangrove tunicate. Enzymes from hydrothermal vent microbes are routinely used in PCR reactions, and marine-derived molecular probes are helping understand the molecular basis of disease processes. Advances in aquaculture biotechnology have resulted in more efficient production of finfish and shellfish for human consumption, and polyunsaturated fatty acids from marine microalgae are used as nutritional supplements for adults and infants. Rapid diagnostic tools have been developed to monitor toxins in the environment and in seafood, and genetic fingerprinting techniques are helping to control illegal trade of threatened marine species. In the future, multidisciplinary programs in oceans and human health should focus not only on microbial pathogens and harmful algal bloom toxins but also on discovery of new chemicals to prevent or treat human diseases. And the development of biological and biochemical sensors to detect pathogens, contaminants, and toxins and to monitor human and environmental health indicators in the marine environment should be a very high priority in the establishment of U.S. coastal ocean observing systems.

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Goddard, Stephen. "Marine biotechnology: Emerging opportunities and future perspectives." Journal of Agricultural and Marine Sciences [JAMS] 20 (January 1, 2015): 7. http://dx.doi.org/10.24200/jams.vol20iss0pp7-7.

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The rapid growth of genetic, cellular and molecular technologies is enabling scientists to explore and develop marine resources for widespread applications in the food, medical, pharmaceutical, environmental and energy industries. Marine biotechnology products and services were estimated at 2.8 billion euros in 2010, with a cumulative annual growth rate of 4-5% (Marine Board-European Science Foundation, 2010) The Sultanate of Oman occupies a strategic geographical position and has a coastline in excess of 3000km, with the Arabian Sea located to the south and the Sea of Oman and Arabian Gulf to the north. These oceans have rich biodiversity and potential resources which we are only beginning to explore. Based on its marine resources, coupled with a rapidly-growing educational and research infrastructure, the Sultanate of Oman is well positioned to take advantage of the commercial opportunities presented by marine biotechnology. In recognition of potential development an international symposium was organized by the Center of Excellence in Marine Biotechnology, Sultan Qaboos University. One hundred and forty eight delegates attended the meeting, representing 15 countries. In planning the symposium three major themes were identified viz. Marine Biofouling and its Prevention, Fisheries and Aquaculture Biotechnology and Marine Biodiversity and Natural Products. The topics were selected on the basis of current and planned research activity in Oman and elsewhere in the GCC region. Three keynote addresses were presented, 23 oral presentations made and a poster exhibition held. A final session reviewed national and regional issues and the delegates agreed formally on a number of future actions. Full details of the symposium and the results and analysis of a post-symposium survey on the future development of marine biotechnology are given in Goddard et al. (2015).The symposium was supported logistically and financially by Sultan Qaboos University, The Research Council, and the

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Tian, Limei, Yue Yin, Wei Bing, and E. Jin. "Antifouling Technology Trends in Marine Environmental Protection." Journal of Bionic Engineering 18, no. 2 (March 2021): 239–63. http://dx.doi.org/10.1007/s42235-021-0017-z.

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AbstractMarine fouling is a worldwide problem, which is harmful to the global marine ecological environment and economic benefits. The traditional antifouling strategy usually uses toxic antifouling agents, which gradually exposes a serious environmental problem. Therefore, green, long-term, broad-spectrum and eco-friendly antifouling technologies have been the main target of engineers and researchers. In recent years, many eco-friendly antifouling technologies with broad application prospects have been developed based on the low toxicity and non-toxicity antifouling agents and materials. In this review, contemporary eco-friendly antifouling technologies and materials are summarized into bionic antifouling and non-bionic antifouling strategies (2000–2020). Non-bionic antifouling technologies mainly include protein resistant polymers, antifoulant releasing coatings, foul release coatings, conductive antifouling coatings and photodynamic antifouling technology. Bionic antifouling technologies mainly include the simulated shark skin, whale skin, dolphin skin, coral tentacles, lotus leaves and other biology structures. Brief future research directions and challenges are also discussed in the end, and we expect that this review would boost the development of marine antifouling technologies.

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Nicoletti, Rosario, and Francesco Vinale. "Bioactive Compounds from Marine-Derived Aspergillus, Penicillium, Talaromyces and Trichoderma Species." Marine Drugs 16, no. 11 (October 26, 2018): 408. http://dx.doi.org/10.3390/md16110408.

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The impact of bioactive compounds from natural sources on human life, particularly in pharmacology and biotechnology, has challenged the scientific community to explore new environmental contexts and the associated microbial diversity. [...]

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de la Calle, Fernando. "Marine Genetic Resources. A Source of New Drugs The Experience of the Biotechnology Sector." International Journal of Marine and Coastal Law 24, no. 2 (2009): 209–20. http://dx.doi.org/10.1163/157180809x421743.

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AbstractThis article provides an overview of the conversion of marine genetic resources into new drugs. Three marine organisms suitable for application in human health and steps in the drug discovery process are described. Specific supply problems resulting from the minute concentration of required compounds for medicine in the natural marine source are examined. Three case studies illustrate different strategies enabling an industrial-scale production: chemical synthesis, biotechnology and fermentation. Future concepts for marine scientific research which could lead to new medical applications are considered. Besides research in unexplored deep sea areas, the “metagenomic approach” particularly might lead to significant new achievements. This DNA analysis of marine organisms facilitates the drug discovery process because it requires significantly less marine material than current approaches. Because this process, starting with the search for bioactive molecules and continuing with the production of drug-like molecules before finally reaching the status of medicine, can take up to 20 years, the development of medicine is a very long and risky venture.

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Schmidt, Eric W. "From chemical structure to environmental biosynthetic pathways: navigating marine invertebrate–bacteria associations." Trends in Biotechnology 23, no. 9 (September 2005): 437–40. http://dx.doi.org/10.1016/j.tibtech.2005.07.002.

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Kalogerakis, Nicolas, Johanne Arff, Ibrahim M. Banat, Ole Jacob Broch, Daniele Daffonchio, Torgeir Edvardsen, Harkaitz Eguiraun, et al. "The role of environmental biotechnology in exploring, exploiting, monitoring, preserving, protecting and decontaminating the marine environment." New Biotechnology 32, no. 1 (January 2015): 157–67. http://dx.doi.org/10.1016/j.nbt.2014.03.007.

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Nielsen, Michael, Lars Hauer Larsen, Mike S. M. Jetten, and Niels Peter Revsbech. "Bacterium-Based NO2− Biosensor for Environmental Applications." Applied and Environmental Microbiology 70, no. 11 (November 2004): 6551–58. http://dx.doi.org/10.1128/aem.70.11.6551-6558.2004.

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ABSTRACT A sensitive NO2 − biosensor that is based on bacterial reduction of NO2 − to N2O and subsequent detection of the N2O by a built-in electrochemical N2O sensor was developed. Four different denitrifying organisms lacking NO3 − reductase activity were assessed for use in the biosensor. The relevant physiological aspects examined included denitrifying characteristics, growth rate, NO2 − tolerance, and temperature and salinity effects on the growth rate. Two organisms were successfully used in the biosensor. The preferred organism was Stenotrophomonas nitritireducens, which is an organism with a denitrifying pathway deficient in both NO3 − and N2O reductases. Alternatively Alcaligenes faecalis could be used when acetylene was added to inhibit its N2O reductase. The macroscale biosensors constructed exhibited a linear NO2 − response at concentrations up to 1 to 2 mM. The detection limit was around 1 μM NO2 −, and the 90% response time was 0.5 to 3 min. The sensor signal was specific for NO2 −, and interference was observed only with NH2OH, NO, N2O, and H2S. The sensor signal was affected by changes in temperature and salinity, and calibration had to be performed in a system with a temperature and an ionic strength comparable to those of the medium analyzed. A broad range of water bodies could be analyzed with the biosensor, including freshwater systems, marine systems, and oxic-anoxic wastewaters. The NO2 − biosensor was successfully used for long-term online monitoring in wastewater. Microscale versions of the NO2 − biosensor were constructed and used to measure NO2 − profiles in marine sediment.

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Murray, Shauna A., Maria Wiese, Anke Stüken, Steve Brett, Ralf Kellmann, Gustaaf Hallegraeff, and Brett A. Neilan. "sxtA-Based Quantitative Molecular Assay To Identify Saxitoxin-Producing Harmful Algal Blooms in Marine Waters." Applied and Environmental Microbiology 77, no. 19 (August 12, 2011): 7050–57. http://dx.doi.org/10.1128/aem.05308-11.

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ABSTRACTThe recent identification of genes involved in the production of the potent neurotoxin and keystone metabolite saxitoxin (STX) in marine eukaryotic phytoplankton has allowed us for the first time to develop molecular genetic methods to investigate the chemical ecology of harmful algal bloomsin situ. We present a novel method for detecting and quantifying the potential for STX production in marine environmental samples. Our assay detects a domain of the genesxtAthat encodes a unique enzyme putatively involved in thesxtpathway in marine dinoflagellates,sxtA4. A product of the correct size was recovered from nine strains of four species of STX-producingAlexandriumandGymnodinium catenatumand was not detected in the non-STX-producingAlexandriumspecies, other dinoflagellate cultures, or an environmental sample that did not contain known STX-producing species. However,sxtA4was also detected in the non-STX-producing strain ofAlexandrium tamarense, Tasmanian ribotype. We investigated the copy number ofsxtA4in three strains ofAlexandrium catenellaand found it to be relatively constant among strains. Using our novel method, we detected and quantifiedsxtA4in three environmental blooms ofAlexandrium catenellathat led to STX uptake in oysters. We conclude that this method shows promise as an accurate, fast, and cost-effective means of quantifying the potential for STX production in marine samples and will be useful for biological oceanographic research and harmful algal bloom monitoring.

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Labonté, Jessica M., Karen E. Reid, and Curtis A. Suttle. "Phylogenetic Analysis Indicates Evolutionary Diversity and Environmental Segregation of Marine Podovirus DNA Polymerase Gene Sequences." Applied and Environmental Microbiology 75, no. 11 (April 10, 2009): 3634–40. http://dx.doi.org/10.1128/aem.02317-08.

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ABSTRACT The distribution of viral genotypes in the ocean and their evolutionary relatedness remain poorly constrained. This paper presents data on the genetic diversity and evolutionary relationships of 1.2-kb DNA polymerase (pol) gene fragments from podoviruses. A newly designed set of PCR primers was used to amplify DNA directly from coastal sediment and water samples collected from inlets adjacent to the Strait of Georgia, British Columbia, Canada, and from the northeastern Gulf of Mexico. Restriction fragment length polymorphism analysis of 160 cloned PCR products revealed 29 distinct operational taxonomic units (OTUs), with OTUs within a site typically being more similar than those among sites. Phylogenetic analysis of the DNA pol gene fragments demonstrated high similarity between some environmental sequences and sequences from the marine podoviruses roseophage SIO1 and cyanophage P60, while others were not closely related to sequences from cultured phages. Interrogation of the CAMERA database for sequences from metagenomics data demonstrated that the amplified sequences were representative of the diversity of podovirus pol sequences found in marine samples. Our results indicate high genetic diversity within marine podovirus communities within a small geographic region and demonstrate that the diversity of environmental polymerase gene sequences for podoviruses is far more extensive than previously recognized.

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Kurihara, Masaru, Hiromu Takeuchi, and Yohito Ito. "A Reliable Seawater Desalination System Based on Membrane Technology and Biotechnology Considering Reduction of the Environmental Impact." Environments 5, no. 12 (December 3, 2018): 127. http://dx.doi.org/10.3390/environments5120127.

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The application of seawater desalination technology using a reverse osmosis (RO) membrane has been expanding because it requires less energy compared with other distillation methods. Even in Middle Eastern countries where energy costs are lower such as Saudi Arabia, UAE, Qatar, and Kuwait, almost all desalination plants where only water production is required have adopted the RO method. However, large plants in excess of half mega-ton size are required, and Seawater Reverse Osmosis (SWRO) operation lacks reliability due to heavy biofouling and large amounts of briny discharge contaminated with chemicals. For reliable desalination systems with lower environmental impact, membrane-processing technology, including biotechnology (such as marine bacteria), has been examined as national research in Japan in the “Mega-ton Water System” project. We examined the influence of chlorination on marine bacteria using the fluorescence microscopic observation method and found that the effect of chlorination is limited. Chlorination sterilization triggers biofouling and sodium bisulfate (SBS) addition as a de-chlorinating agent also triggers biofouling, so a process with no chlorine or SBS addition would reduce biofouling. As polyamide SWRO membranes have low chlorine resistivity, such a process would enable longer membrane life in real plants. We used a biofouling monitoring technology, the Membrane Biofilm Formation Rate (mBFR), to design a process that involves no chlorine or SBS addition and verified it in the Arabian Gulf Sea, of Saudi Arabia, which is one of the most difficult and challenging seawaters in which to control biofouling. Furthermore, by minimizing the addition of a sterilizer, the desalination system became more environmentally friendly.

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Mitchell, Emily G., Nikolai Bobkov, Natalia Bykova, Alavya Dhungana, Anton V. Kolesnikov, Ian R. P. Hogarth, Alexander G. Liu, et al. "The influence of environmental setting on the community ecology of Ediacaran organisms." Interface Focus 10, no. 4 (June 12, 2020): 20190109. http://dx.doi.org/10.1098/rsfs.2019.0109.

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The broad-scale environment plays a substantial role in shaping modern marine ecosystems, but the degree to which palaeocommunities were influenced by their environment is unclear. To investigate how broad-scale environment influenced the community ecology of early animal ecosystems, we employed spatial point process analyses (SPPA) to examine the community structure of seven late Ediacaran (558–550 Ma) bedding-plane assemblages drawn from a range of environmental settings and global localities. The studied palaeocommunities exhibit marked differences in the response of their component taxa to sub-metre-scale habitat heterogeneities on the seafloor. Shallow-marine (nearshore) palaeocommunities were heavily influenced by local habitat heterogeneities, in contrast to their deeper-water counterparts. The local patchiness within shallow-water communities may have been further accentuated by the presence of grazers and detritivores, whose behaviours potentially initiated a propagation of increasing habitat heterogeneity of benthic communities from shallow to deep-marine depositional environments. Higher species richness in shallow-water Ediacaran assemblages compared to deep-water counterparts across the studied time-interval could have been driven by this environmental patchiness, because habitat heterogeneities increase species richness in modern marine environments. Our results provide quantitative support for the ‘Savannah’ hypothesis for early animal diversification—whereby Ediacaran diversification was driven by patchiness in the local benthic environment.

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Cottrell, Matthew T., and David L. Kirchman. "Transcriptional Control in Marine Copiotrophic and Oligotrophic Bacteria with Streamlined Genomes." Applied and Environmental Microbiology 82, no. 19 (July 29, 2016): 6010–18. http://dx.doi.org/10.1128/aem.01299-16.

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ABSTRACTBacteria often respond to environmental stimuli using transcriptional control, but this may not be the case for marine bacteria such as “CandidatusPelagibacter ubique,” a cultivated representative of the SAR11 clade, the most abundant organism in the ocean. This bacterium has a small, streamlined genome and an unusually low number of transcriptional regulators, suggesting that transcriptional control is low inPelagibacterand limits its response to environmental conditions. Transcriptome sequencing during batch culture growth revealed that only 0.1% of protein-encoding genes appear to be under transcriptional control inPelagibacterand in another oligotroph (SAR92) whereas >10% of genes were under transcriptional control in the copiotrophsPolaribactersp. strain MED152 andRuegeria pomeroyi. When growth levels changed, transcript levels remained steady inPelagibacterand SAR92 but shifted in MED152 andR. pomeroyi. Transcript abundances per cell, determined using an internal RNA sequencing standard, were low (<1 transcript per cell) for all but a few of the most highly transcribed genes in all four taxa, and there was no correlation between transcript abundances per cell and shifts in the levels of transcription. These results suggest that low transcriptional control contributes to the success ofPelagibacterand possibly other oligotrophic microbes that dominate microbial communities in the oceans.IMPORTANCEDiverse heterotrophic bacteria drive biogeochemical cycling in the ocean. The most abundant types of marine bacteria are oligotrophs with small, streamlined genomes. The metabolic controls that regulate the response of oligotrophic bacteria to environmental conditions remain unclear. Our results reveal that transcriptional control is lower in marine oligotrophic bacteria than in marine copiotrophic bacteria. Although responses of bacteria to environmental conditions are commonly regulated at the level of transcription, metabolism in the most abundant bacteria in the ocean appears to be regulated by other mechanisms.

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Di Donato, Paola, Andrea Buono, Annarita Poli, Ilaria Finore, Gennaro Abbamondi, Barbara Nicolaus, and Licia Lama. "Exploring Marine Environments for the Identification of Extremophiles and Their Enzymes for Sustainable and Green Bioprocesses." Sustainability 11, no. 1 (December 28, 2018): 149. http://dx.doi.org/10.3390/su11010149.

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Sea environments harbor a wide variety of life forms that have adapted to live in hard and sometimes extreme conditions. Among the marine living organisms, extremophiles represent a group of microorganisms that attract increasing interest in relation to their ability to produce an array of molecules that enable them to thrive in almost every marine environment. Extremophiles can be found in virtually every extreme environment on Earth, since they can tolerate very harsh environmental conditions in terms of temperature, pH, pressure, radiation, etc. Marine extremophiles are the focus of growing interest in relation to their ability to produce biotechnologically useful enzymes, the so-called extremozymes. Thanks to their resistance to temperature, pH, salt, and pollutants, marine extremozymes are promising biocatalysts for new and sustainable industrial processes, thus representing an opportunity for several biotechnological applications. Since the marine microbioma, i.e., the complex of microorganisms living in sea environments, is still largely unexplored finding new species is a central issue for green biotechnology. Here we described the main marine environments where extremophiles can be found, some existing or potential biotechnological applications of marine extremozymes for biofuels production and bioremediation, and some possible approaches for the search of new biotechnologically useful species from marine environments.

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Michotey, Valérie, Vincent Méjean, and Patricia Bonin. "Comparison of Methods for Quantification of Cytochrome cd1-Denitrifying Bacteria in Environmental Marine Samples." Applied and Environmental Microbiology 66, no. 4 (April 1, 2000): 1564–71. http://dx.doi.org/10.1128/aem.66.4.1564-1571.2000.

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ABSTRACT Two PCR primer sets were developed for the detection and quantification of cytochrome cd 1-denitrifying bacteria in environmental marine samples. The specificity and sensitivity of these primers were tested. Both primer sets were suitable for detection, but only one set, cd3F–cd4R, was suitable for the quantification and enumeration of the functional community using most-probable-number PCR and competitive PCR techniques. Quantification of cytochrome cd 1 denitrifiers taken from marine sediment and water samples was achieved using two different molecular techniques which target the nirS gene, and the results were compared to those obtained by using the classical cultivation method. Enumerations using both molecular techniques yielded similar results in seawater and sediment samples. However, both molecular techniques showed 1,000 or 10 times more cytochromecd 1 denitrifiers in the sediment or water samples, respectively, than were found by use of the conventional cultivation method for counting.

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Ambrosino, Luca, Michael Tangherlini, Chiara Colantuono, Alfonso Esposito, Mara Sangiovanni, Marco Miralto, Clementina Sansone, and Maria Luisa Chiusano. "Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives." Marine Drugs 17, no. 10 (October 11, 2019): 576. http://dx.doi.org/10.3390/md17100576.

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The sea represents a major source of biodiversity. It exhibits many different ecosystems in a huge variety of environmental conditions where marine organisms have evolved with extensive diversification of structures and functions, making the marine environment a treasure trove of molecules with potential for biotechnological applications and innovation in many different areas. Rapid progress of the omics sciences has revealed novel opportunities to advance the knowledge of biological systems, paving the way for an unprecedented revolution in the field and expanding marine research from model organisms to an increasing number of marine species. Multi-level approaches based on molecular investigations at genomic, metagenomic, transcriptomic, metatranscriptomic, proteomic, and metabolomic levels are essential to discover marine resources and further explore key molecular processes involved in their production and action. As a consequence, omics approaches, accompanied by the associated bioinformatic resources and computational tools for molecular analyses and modeling, are boosting the rapid advancement of biotechnologies. In this review, we provide an overview of the most relevant bioinformatic resources and major approaches, highlighting perspectives and bottlenecks for an appropriate exploitation of these opportunities for biotechnology applications from marine resources.

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Grüntzig, Verónica, Stephen C. Nold, Jizhong Zhou, and James M. Tiedje. "Pseudomonas stutzeri Nitrite Reductase Gene Abundance in Environmental Samples Measured by Real-Time PCR." Applied and Environmental Microbiology 67, no. 2 (February 1, 2001): 760–68. http://dx.doi.org/10.1128/aem.67.2.760-768.2001.

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ABSTRACT We used real-time PCR to quantify the denitrifying nitrite reductase gene (nirS), a functional gene of biogeochemical significance. The assay was tested in vitro and applied to environmental samples. The primer-probe set selected was specific fornirS sequences that corresponded approximately to thePseudomonas stutzeri species. The assay was linear from 1 to 106 gene copies (r 2 = 0.999). Variability at low gene concentrations did not allow detection of twofold differences in gene copy number at less than 100 copies. DNA spiking and cell-addition experiments gave predicted results, suggesting that this assay provides an accurate measure of P. stutzeri nirS abundance in environmental samples. AlthoughP. stutzeri abundance was high in lake sediment and groundwater samples, we detected low or no abundance of this species in marine sediment samples from Puget Sound (Wash.) and from the Washington ocean margin. These results suggest that P. stutzeri may not be a dominant marine denitrifier.

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van der Maarel, Marc J. E. C., Rebekka R. E. Artz, René Haanstra, and Larry J. Forney. "Association of Marine Archaea with the Digestive Tracts of Two Marine Fish Species." Applied and Environmental Microbiology 64, no. 8 (August 1, 1998): 2894–98. http://dx.doi.org/10.1128/aem.64.8.2894-2898.1998.

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ABSTRACT Recent studies have shown that archaea which were always thought to live under strict anoxic or extreme environmental conditions are also present in cold, oxygenated seawater, soils, the digestive tract of a holothurian deep-sea-deposit feeder, and a marine sponge. In this study, we show, by using PCR-mediated screening in other marine eukaryotes, that marine archaea are also present in the digestive tracts of flounder and grey mullet, two fish species common in the North Sea, in fecal samples of flounder, and in suspended particulate matter of the North Sea water column. No marine archaea could be detected in the digestive tracts of mussels or the fecal pellets of a copepod species. The archaeal 16S ribosomal DNA clone libraries of feces of flounder and the contents of the digestive tracts of grey mullet and flounder were dominated by group II marine archaea. The marine archaeal clones derived from flounder and grey mullet digestive tracts and feces formed a distinct cluster within the group II marine archaea, with 76.7 to 89.8% similarity to previously described group II clones. Fingerprinting of the archaeal community of flounder digestive tract contents and feces by terminal restriction fragment length polymorphism of archaeal 16S rRNA genes after restriction withHhaI showed a dominant fragment at 249 bp, which is likely to be derived from group II marine archaea. Clones of marine archaea that were closely related to the fish-associated marine archaea clones were obtained from suspended particulate matter of the water column at two stations in the North Sea. Terminal restriction fragment length polymorphism fingerprinting of the archaeal community present in suspended particulate matter showed the same fragment pattern as was found for the archaeal community of the flounder digestive tract contents and feces. These data demonstrate that marine archaea are present in the digestive tracts and feces of very common marine fish. It is possible that the marine archaea associated with the digestive tracts of marine fish are liberated into the water column through the feces and subsequently contribute to the marine archaeal community of suspended particulate matter.

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Eskova, Alena I., Boris G. Andryukov, Anatoli A. Yakovlev, Alexandra V. Kim, Anna L. Ponomareva, and Vera S. Obuhova. "Horizontal Transfer of Virulence Factors by Pathogenic Enterobacteria to Marine Saprotrophic Bacteria during Co-Cultivation in Biofilm." BioTech 11, no. 2 (May 24, 2022): 17. http://dx.doi.org/10.3390/biotech11020017.

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Environmental problems associated with marine pollution and climate warming create favorable conditions for the penetration and survival of pathogenic bacteria in marine ecosystems. These microorganisms have interspecific competitive interactions with marine bacteria. Co-culture, as an important research strategy that mimics the natural environment of bacteria, can activate silent genes or clusters through interspecies interactions. The authors used modern biotechnology of co-cultivation to dynamically study intercellular interactions between different taxa of bacteria—pathogenic enterobacteria Yersinia pseudotuberculosis and Listeria monocytogenes and saprotrophic marine bacteria Bacillus sp. and Pseudomonas japonica isolated in summer from the coastal waters of the recreational areas of the Sea of Japan. The results of the experiments showed that during the formation of polycultural biofilms, horizontal transfer of genes encoding some pathogenicity factors from Y. pseudotuberculosis and L. monocytogenes to marine saprotrophic bacteria with different secretion systems is possible. It was previously thought that this was largely prevented by the type VI secretion system (T6SS) found in marine saprotrophic bacteria. The authors showed for the first time the ability of marine bacteria Bacillus sp. and P. japonica to biofilm formation with pathogenic enterobacteria Y. pseudotuberculosis and L. monocytogenes, saprophytic bacteria with type III secretion system (T3SS). For the first time, a marine saprotrophic strain of Bacillus sp. Revealed manifestations of hyaluronidase, proteolytic and hemolytic activity after cultivation in a polycultural biofilm with listeria. Saprotrophic marine bacteria that have acquired virulence factors from pathogenic enterobacteria, including antibiotic resistance genes, could potentially play a role in altering the biological properties of other members of the marine microbial community. In addition, given the possible interdomain nature of intercellular gene translocation, acquired virulence factors can be transferred to marine unicellular and multicellular eukaryotes. The results obtained contribute to the paradigm of the epidemiological significance and potential danger of anthropogenic pollution of marine ecosystems, which creates serious problems for public health and the development of marine culture as an important area of economic activity in coastal regions.

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Vogel, Birte Fonnesbech, Hanne Marie Holt, Peter Gerner-Smidt, Anemone Bundvad, Per Søgaard, and Lone Gram. "Homogeneity of Danish Environmental and Clinical Isolates of Shewanella algae." Applied and Environmental Microbiology 66, no. 1 (January 1, 2000): 443–48. http://dx.doi.org/10.1128/aem.66.1.443-448.2000.

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ABSTRACT Danish isolates of Shewanella algae constituted by whole-cell protein profiling a very homogeneous group, and no clear distinction was seen between strains from the marine environment and strains of clinical origin. Although variation between all strains was observed by ribotyping and random amplified polymorphic DNA analysis, no clonal relationship between infective strains was found. From several patients, clonally identical strains of S. algaewere reisolated up to 8 months after the primary isolation, indicating that the same strain may be able to maintain the infection.

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Nayak, Bina, Jennifer Weidhaas, and Valerie J. Harwood. "LA35 Poultry Fecal Marker Persistence Is Correlated with That of Indicators and Pathogens in Environmental Waters." Applied and Environmental Microbiology 81, no. 14 (May 1, 2015): 4616–25. http://dx.doi.org/10.1128/aem.00444-15.

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ABSTRACTDisposal of fecally contaminated poultry litter by land application can deliver pathogens and fecal indicator bacteria (FIB) into receiving waters via runoff. While water quality is regulated by FIB enumeration, FIB testing provides inadequate information about contamination source and health risk. This microbial source tracking (MST) study compared the persistence of theBrevibacteriumsp. strain LA35 16S rRNA gene (marker) for poultry litter with that of pathogens and FIB under outdoor, environmentally relevant conditions in freshwater, marine water, and sediments over 7 days.Salmonella enterica,Campylobacter jejuni,Campylobacter coli,Bacteroidales, and LA35 were enumerated by quantitative PCR (qPCR), andEnterococcusspp. andE. coliwere quantified by culture and qPCR. Unlike the other bacteria,C. jejuniwas not detectable after 48 h. Bacterial levels in the water column consistently declined over time and were highly correlated among species. Survival in sediments ranged from a slow decrease over time to growth, particularly in marine microcosms and forBacteroidales. S. entericaalso grew in marine sediments. Linear decay rates in water (k) ranged from −0.17 day−1for LA35 to −3.12 day−1forC. coli. LA35 levels correlated well with those of other bacteria in the water column but not in sediments. These observations suggest that, particularly in the water column, the fate of LA35 in aquatic environments is similar to that of FIB,C. coli, andSalmonella, supporting the hypothesis that the LA35 marker gene can be a useful tool for evaluating the impact of poultry litter on water quality and human health risk.

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Ahmed, Warish, Christopher Staley, Thomas Kaiser, Michael J. Sadowsky, Sonya Kozak, David Beale, and Stuart Simpson. "Decay of sewage-associated bacterial communities in fresh and marine environmental waters and sediment." Applied Microbiology and Biotechnology 102, no. 16 (June 5, 2018): 7159–70. http://dx.doi.org/10.1007/s00253-018-9112-4.

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Mincer, Tracy J., William Fenical, and Paul R. Jensen. "Culture-Dependent and Culture-Independent Diversity within the Obligate Marine Actinomycete Genus Salinispora." Applied and Environmental Microbiology 71, no. 11 (November 2005): 7019–28. http://dx.doi.org/10.1128/aem.71.11.7019-7028.2005.

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ABSTRACT Salinispora is the first obligate marine genus within the order Actinomycetales and a productive source of biologically active secondary metabolites. Despite a worldwide, tropical or subtropical distribution in marine sediments, only two Salinispora species have thus far been cultivated, suggesting limited species-level diversity. To further explore Salinispora diversity and distributions, the phylogenetic diversity of more than 350 strains isolated from sediments collected around the Bahamas was examined, including strains cultured using new enrichment methods. A culture-independent method, using a Salinispora-specific seminested PCR technique, was used to detect Salinispora from environmental DNA and estimate diversity. Overall, the 16S rRNA gene sequence diversity of cultured strains agreed well with that detected in the environmental clone libraries. Despite extensive effort, no new species level diversity was detected, and 97% of the 105 strains examined by restriction fragment length polymorphism belonged to one phylotype (S. arenicola). New intraspecific diversity was detected in the libraries, including an abundant new phylotype that has yet to be cultured, and a new depth record of 1,100 m was established for the genus. PCR-introduced error, primarily from Taq polymerase, significantly increased clone library sequence diversity and, if not masked from the analyses, would have led to an overestimation of total diversity. An environmental DNA extraction method specific for vegetative cells provided evidence for active actinomycete growth in marine sediments while indicating that a majority of sediment samples contained predominantly Salinispora spores at concentrations that could not be detected in environmental clone libraries. Challenges involved with the direct sequence-based detection of spore-forming microorganisms in environmental samples are discussed.

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Poretsky, Rachel S., Nasreen Bano, Alison Buchan, Gary LeCleir, Jutta Kleikemper, Maria Pickering, Whitney M. Pate, Mary Ann Moran, and James T. Hollibaugh. "Analysis of Microbial Gene Transcripts in Environmental Samples†." Applied and Environmental Microbiology 71, no. 7 (July 2005): 4121–26. http://dx.doi.org/10.1128/aem.71.7.4121-4126.2005.

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ABSTRACT We analyzed gene expression in marine and freshwater bacterioplankton communities by the direct retrieval and analysis of microbial transcripts. Environmental mRNA, obtained from total RNA by subtractive hybridization of rRNA, was reverse transcribed, amplified with random primers, and cloned. Approximately 400 clones were analyzed, of which ∼80% were unambiguously mRNA derived. mRNAs appeared to be from diverse taxonomic groups, including both Bacteria (mainly α- and γ-Proteobacteria) and Archaea (mainly Euryarchaeota). Many transcripts could be linked to environmentally important processes such as sulfur oxidation (soxA), assimilation of C1 compounds (fdh1B), and acquisition of nitrogen via polyamine degradation (aphA). Environmental transcriptomics is a means of exploring functional gene expression within natural microbial communities without bias toward known sequences, and provides a new approach for obtaining community-specific variants of key functional genes.

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Barone, Varrella, Tangherlini, Rastelli, Dell'Anno, Danovaro, and Corinaldesi. "Marine Fungi: Biotechnological Perspectives from Deep-Hypersaline Anoxic Basins." Diversity 11, no. 7 (July 16, 2019): 113. http://dx.doi.org/10.3390/d11070113.

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Deep-sea hypersaline anoxic basins (DHABs) are one of the most hostile environments on Earth. Even though DHABs have hypersaline conditions, anoxia and high hydrostatic pressure, they host incredible microbial biodiversity. Among eukaryotes inhabiting these systems, recent studies demonstrated that fungi are a quantitatively relevant component. Here, fungi can benefit from the accumulation of large amounts of organic material. Marine fungi are also known to produce bioactive molecules. In particular, halophilic and halotolerant fungi are a reservoir of enzymes and secondary metabolites with valuable applications in industrial, pharmaceutical, and environmental biotechnology. Here we report that among the fungal taxa identified from the Mediterranean and Red Sea DHABs, halotolerant halophilic species belonging to the genera Aspergillus and Penicillium can be used or screened for enzymes and bioactive molecules. Fungi living in DHABs can extend our knowledge about the limits of life, and the discovery of new species and molecules from these environments can have high biotechnological potential.

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Scheinin, M., U. Riebesell, T. A. Rynearson, K. T. Lohbeck, and S. Collins. "Experimental evolution gone wild." Journal of The Royal Society Interface 12, no. 106 (May 2015): 20150056. http://dx.doi.org/10.1098/rsif.2015.0056.

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Because of their large population sizes and rapid cell division rates, marine microbes have, or can generate, ample variation to fuel evolution over a few weeks or months, and subsequently have the potential to evolve in response to global change. Here we measure evolution in the marine diatom Skeletonema marinoi evolved in a natural plankton community in CO 2 -enriched mesocosms deployed in situ . Mesocosm enclosures are typically used to study how the species composition and biogeochemistry of marine communities respond to environmental shifts, but have not been used for experimental evolution to date. Using this approach, we detect a large evolutionary response to CO 2 enrichment in a focal marine diatom, where population growth rate increased by 1.3-fold in high CO 2 -evolved lineages. This study opens an exciting new possibility of carrying out in situ evolution experiments to understand how marine microbial communities evolve in response to environmental change.

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Iraninasab, Sudabeh, Sana Sharifian, Ahmad Homaei, Mozafar Bagherzadeh Homaee, Tanvi Sharma, Ashok Kumar Nadda, John F. Kennedy, Muhammad Bilal, and Hafiz M. N. Iqbal. "Emerging trends in environmental and industrial applications of marine carbonic anhydrase: a review." Bioprocess and Biosystems Engineering 45, no. 3 (November 25, 2021): 431–51. http://dx.doi.org/10.1007/s00449-021-02667-8.

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Khemakhem, Walid, Emna Ammar, and Amina Bakhrouf. "Effect of Environmental Conditions on Hydrophobicity of Marine Bacteria Adapted to Textile Effluent Treatment." World Journal of Microbiology and Biotechnology 21, no. 8-9 (December 2005): 1623–31. http://dx.doi.org/10.1007/s11274-005-8537-y.

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Shaikh, Sohail F., Harold F. Mazo-Mantilla, Nadeem Qaiser, Sherjeel M. Khan, Joanna M. Nassar, Nathan R. Geraldi, Carlos M. Duarte, and Muhammad M. Hussain. "Environmental Monitoring: Noninvasive Featherlight Wearable Compliant “Marine Skin”: Standalone Multisensory System for Deep-Sea Environmental Monitoring (Small 10/2019)." Small 15, no. 10 (March 2019): 1970051. http://dx.doi.org/10.1002/smll.201970051.

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Off, Sandra, Mashal Alawi, and Eva Spieck. "Enrichment and Physiological Characterization of a Novel Nitrospira-Like Bacterium Obtained from a Marine Sponge." Applied and Environmental Microbiology 76, no. 14 (May 28, 2010): 4640–46. http://dx.doi.org/10.1128/aem.00320-10.

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ABSTRACT Members of the nitrite-oxidizing genus Nitrospira are most likely responsible for the second step of nitrification, the conversion of nitrite (NO2 −) to nitrate (NO3 −), within various sponges. We succeeded in obtaining an enrichment culture of Nitrospira derived from the mesohyl of the marine sponge Aplysina aerophoba using a traditional cultivation approach. Electron microscopy gave first evidence of the shape and ultrastructure of this novel marine Nitrospira-like bacterium (culture Aa01). We characterized these bacteria physiologically with regard to optimal incubation conditions, especially the temperature and substrate range in comparison to other Nitrospira cultures. Best growth was obtained at temperatures between 28°C and 30°C in mineral medium with 70% North Sea water and a substrate concentration of 0.5 mM nitrite under microaerophilic conditions. The Nitrospira culture Aa01 is very sensitive against nitrite, because concentrations higher than 1.5 mM resulted in a complete inhibition of growth. Sequence analyses of the 16S rRNA gene revealed that the novel Nitrospira-like bacterium is separated from the sponge-specific subcluster and falls together with an environmental clone from Mediterranean sediments (98.6% similarity). The next taxonomically described species Nitrospira marina is only distantly related, with 94.6% sequence similarity, and therefore the culture Aa01 represents a novel species of nitrite-oxidizing bacteria.

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Williams, Tiffany C., Mesrop Ayrapetyan, and James D. Oliver. "Implications of Chitin Attachment for the Environmental Persistence and Clinical Nature of the Human Pathogen Vibrio vulnificus." Applied and Environmental Microbiology 80, no. 5 (December 20, 2013): 1580–87. http://dx.doi.org/10.1128/aem.03811-13.

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ABSTRACTVibrio vulnificusnaturally inhabits a variety of aquatic organisms, including oysters, and is the leading cause of seafood-related death in the United States. Strains of this bacterium are genetically classified into environmental (E) and clinical (C) genotypes, which correlate with source of isolation. E-genotype strains integrate into marine aggregates more efficiently than do C-genotype strains, leading to a greater uptake of strains of this genotype by oysters feeding on these aggregates. The causes of this increased integration of E-type strains into marine “snow” have not been demonstrated. Here, we further investigate the physiological and genetic causalities for this genotypic heterogeneity by examining the ability of strains of each genotype to attach to chitin, a major constituent of marine snow. We found that E-genotype strains attach to chitin with significantly greater efficiency than do C-genotype strains when incubated at 20°C. Type IV pili were implicated in chitin adherence, and even in the absence of chitin, the expression level of type IV pilin genes (pilA,pilD, andmshA) was found to be inherently higher by E genotypes than by C genotypes. In contrast, the level of expression ofN-acetylglucosamine binding protein A (gbpA) was significantly higher in C-genotype strains. Interestingly, incubation at a clinically relevant temperature (37°C) resulted in a significant increase in C-genotype attachment to chitin, which subsequently provided a protective effect against exposure to acid or bile, thus offering a clue into their increased incidence in human infections. This study suggests that C- and E-genotype strains have intrinsically divergent physiological programs, which may help explain the observed differences in the ecology and pathogenic potential between these two genotypes.

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Amachi, Seigo, Yoichi Kamagata, Takahiro Kanagawa, and Yasuyuki Muramatsu. "Bacteria Mediate Methylation of Iodine in Marine and Terrestrial Environments." Applied and Environmental Microbiology 67, no. 6 (June 1, 2001): 2718–22. http://dx.doi.org/10.1128/aem.67.6.2718-2722.2001.

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ABSTRACT Methyl iodide (CH3I) plays an important role in the natural iodine cycle and participates in atmospheric ozone destruction. However, the main source of this compound in nature is still unclear. Here we report that a wide variety of bacteria including terrestrial and marine bacteria are capable of methylating the environmental level of iodide (0.1 μM). Of the strains tested, Rhizobium sp. strain MRCD 19 was chosen for further analysis, and it was found that the cell extract catalyzed the methylation of iodide withS-adenosyl-l-methionine as the methyl donor. These results strongly indicate that bacteria contribute to iodine transfer from the terrestrial and marine ecosystems into the atmosphere.

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Sassoubre, Lauren M., Kevan M. Yamahara, and Alexandria B. Boehm. "Temporal Stability of the Microbial Community in Sewage-Polluted Seawater Exposed to Natural Sunlight Cycles and Marine Microbiota." Applied and Environmental Microbiology 81, no. 6 (January 9, 2015): 2107–16. http://dx.doi.org/10.1128/aem.03950-14.

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ABSTRACTBillions of gallons of untreated wastewater enter the coastal ocean each year. Once sewage microorganisms are in the marine environment, they are exposed to environmental stressors, such as sunlight and predation. Previous research has investigated the fate of individual sewage microorganisms in seawater but not the entire sewage microbial community. The present study used next-generation sequencing (NGS) to examine how the microbial community in sewage-impacted seawater changes over 48 h when exposed to natural sunlight cycles and marine microbiota. We compared the results from microcosms composed of unfiltered seawater (containing naturally occurring marine microbiota) and filtered seawater (containing no marine microbiota) to investigate the effect of marine microbiota. We also compared the results from microcosms that were exposed to natural sunlight cycles with those from microcosms kept in the dark to investigate the effect of sunlight. The microbial community composition and the relative abundance of operational taxonomic units (OTUs) changed over 48 h in all microcosms. Exposure to sunlight had a significant effect on both community composition and OTU abundance. The effect of marine microbiota, however, was minimal. The proportion of sewage-derived microorganisms present in the microcosms decreased rapidly within 48 h, and the decrease was the most pronounced in the presence of both sunlight and marine microbiota, where the proportion decreased from 85% to 3% of the total microbial community. The results from this study demonstrate the strong effect that sunlight has on microbial community composition, as measured by NGS, and the importance of considering temporal effects in future applications of NGS to identify microbial pollution sources.

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Sjöstedt, Johanna, Per Koch-Schmidt, Mikael Pontarp, Björn Canbäck, Anders Tunlid, Per Lundberg, Åke Hagström, and Lasse Riemann. "Recruitment of Members from the Rare Biosphere of Marine Bacterioplankton Communities after an Environmental Disturbance." Applied and Environmental Microbiology 78, no. 5 (December 22, 2011): 1361–69. http://dx.doi.org/10.1128/aem.05542-11.

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ABSTRACTA bacterial community may be resistant to environmental disturbances if some of its species show metabolic flexibility and physiological tolerance to the changing conditions. Alternatively, disturbances can change the composition of the community and thereby potentially affect ecosystem processes. The impact of disturbance on the composition of bacterioplankton communities was examined in continuous seawater cultures. Bacterial assemblages from geographically closely connected areas, the Baltic Sea (salinity 7 and high dissolved organic carbon [DOC]) and Skagerrak (salinity 28 and low DOC), were exposed to gradual opposing changes in salinity and DOC over a 3-week period such that the Baltic community was exposed to Skagerrak salinity and DOC and vice versa. Denaturing gradient gel electrophoresis and clone libraries of PCR-amplified 16S rRNA genes showed that the composition of the transplanted communities differed significantly from those held at constant salinity. Despite this, the growth yields (number of cells ml−1) were similar, which suggests similar levels of substrate utilization. Deep 454 pyrosequencing of 16S rRNA genes showed that the composition of the disturbed communities had changed due to the recruitment of phylotypes present in the rare biosphere of the original community. The study shows that members of the rare biosphere can become abundant in a bacterioplankton community after disturbance and that those bacteria can have important roles in maintaining ecosystem processes.

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Shaikh, Sohail F., Harold F. Mazo-Mantilla, Nadeem Qaiser, Sherjeel M. Khan, Joanna M. Nassar, Nathan R. Geraldi, Carlos M. Duarte, and Muhammad M. Hussain. "Noninvasive Featherlight Wearable Compliant “Marine Skin”: Standalone Multisensory System for Deep-Sea Environmental Monitoring." Small 15, no. 10 (February 1, 2019): 1804385. http://dx.doi.org/10.1002/smll.201804385.

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Yutin, Natalya, Marcelino T. Suzuki, and Oded Béjà. "Novel Primers Reveal Wider Diversity among Marine Aerobic Anoxygenic Phototrophs." Applied and Environmental Microbiology 71, no. 12 (December 2005): 8958–62. http://dx.doi.org/10.1128/aem.71.12.8958-8962.2005.

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ABSTRACT Aerobic anoxygenic phototrophic bacteria (AAnPs) were previously proposed to account for up to 11% of marine bacterioplankton and to potentially have great ecological importance in the world's oceans. Our data show that previously used primers based on the M subunit of anoxygenic photosynthetic reaction center genes (pufM) do not comprehensively identify the diversity of AAnPs in the ocean. We have designed and tested a new set of pufM-specific primers and revealed several new AAnP variants in environmental DNA samples and genomic libraries.

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Watanabe, Yuuki Y., and Yannis P. Papastamatiou. "Biologging and Biotelemetry: Tools for Understanding the Lives and Environments of Marine Animals." Annual Review of Animal Biosciences 11, no. 1 (February 15, 2023): 247–67. http://dx.doi.org/10.1146/annurev-animal-050322-073657.

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Addressing important questions in animal ecology, physiology, and environmental science often requires in situ information from wild animals. This difficulty is being overcome by biologging and biotelemetry, or the use of miniaturized animal-borne sensors. Although early studies recorded only simple parameters of animal movement, advanced devices and analytical methods can now provide rich information on individual and group behavior, internal states, and the surrounding environment of free-ranging animals, especially those in marine systems. We summarize the history of technologies used to track marine animals. We then identify seven major research categories of marine biologging and biotelemetry and explain significant achievements, as well as future opportunities. Big data approaches via international collaborations will be key to tackling global environmental issues (e.g., climate change impacts), and curiosity about the secret lives of marine animals will also remain a major driver of biologging and biotelemetry studies.

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Hagström, Åke, Thomas Pommier, Forest Rohwer, Karin Simu, Willem Stolte, Dominika Svensson, and Ulla Li Zweifel. "Use of 16S Ribosomal DNA for Delineation of Marine Bacterioplankton Species." Applied and Environmental Microbiology 68, no. 7 (July 2002): 3628–33. http://dx.doi.org/10.1128/aem.68.7.3628-3633.2002.

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ABSTRACT All of the marine bacterioplankton-derived 16S ribosomal DNA sequences previously deposited in GenBank were reanalyzed to determine the number of bacterial species in the oceanic surface waters. These sequences have been entered into the database since 1990. The rate of new additions reached a peak in 1999 and subsequently leveled off, suggesting that much of the marine microbial species richness has been sampled. When the GenBank sequences were dereplicated by using 97% similarity as a cutoff, 1,117 unique ribotypes were found. Of the unique sequences, 609 came from uncultured environmental clones and 508 came from cultured bacteria. We conclude that the apparent bacterioplankton species richness is relatively low.

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Lévy, Marina, Oliver Jahn, Stephanie Dutkiewicz, Michael J. Follows, and Francesco d'Ovidio. "The dynamical landscape of marine phytoplankton diversity." Journal of The Royal Society Interface 12, no. 111 (October 2015): 20150481. http://dx.doi.org/10.1098/rsif.2015.0481.

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Observations suggest that the landscape of marine phytoplankton assemblage might be strongly heterogeneous at the dynamical mesoscale and submesoscale (10–100 km, days to months), with potential consequences in terms of global diversity and carbon export. But these variations are not well documented as synoptic taxonomic data are difficult to acquire. Here, we examine how phytoplankton assemblage and diversity vary between mesoscale eddies and submesoscale fronts. We use a multi-phytoplankton numerical model embedded in a mesoscale flow representative of the North Atlantic. Our model results suggest that the mesoscale flow dynamically distorts the niches predefined by environmental contrasts at the basin scale and that the phytoplankton diversity landscape varies over temporal and spatial scales that are one order of magnitude smaller than those of the basin-scale environmental conditions. We find that any assemblage and any level of diversity can occur in eddies and fronts. However, on a statistical level, the results suggest a tendency for larger diversity and more fast-growing types at fronts, where nutrient supplies are larger and where populations of adjacent water masses are constantly brought into contact; and lower diversity in the core of eddies, where water masses are kept isolated long enough to enable competitive exclusion.

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Mehrshad, Maliheh, Mohammad Ali Amoozegar, Rohit Ghai, Seyed Abolhassan Shahzadeh Fazeli, and Francisco Rodriguez-Valera. "Genome Reconstruction from Metagenomic Data Sets Reveals Novel Microbes in the Brackish Waters of the Caspian Sea." Applied and Environmental Microbiology 82, no. 5 (January 4, 2016): 1599–612. http://dx.doi.org/10.1128/aem.03381-15.

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ABSTRACTWe present here the findings from a study of the microbiome of the southern basin of the Caspian Sea, the largest water body on Earth disconnected from any ocean and a brackish inland sea. By high-throughput metagenomics, we were able to reconstruct the genomes of representative microbes. The gross community structure (at the phylum level) was different from the structure of typical marine and freshwater communities in temperate open oceans, with the Caspian Sea having freshwater-like amounts ofActinobacteriaandAlphaproteobacteria, whileGammaproteobacteriaandBetaproteobacteriawere present at intermediate levels. We assembled the genomes of several groups and provide detailed descriptions of partial genomes fromActinobacteria,Thaumarchaea, andAlphaproteobacteria. Most belonged to hitherto unknown groups, although they were related to either marine or freshwater groups. The phylogenetic placement of the Caspian genomes indicates that the organisms have multiple and separate phylogenetic origins and that they are related to organisms with both freshwater and marine lineages. Comparative recruitment from global aquatic metagenomes indicated that most Caspian microbes are endemic. However, some Caspian genomes were recruited significantly from either marine water (a member of theAlphaproteobacteria) or freshwater (a member of theActinobacteria). Reciprocally, some genomes of other origins, such as the marine thaumarchaeon “CandidatusNitrosopelagicus” or the actinobacterium “CandidatusActinomarina,” were recruited from the Caspian Sea, indicating some degree of overlap with the microbiota of other water bodies. Some of these microbes seem to have a remarkably widespread geographic and environmental distribution.

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Martin, Patrick, and Benjamin A. S. Van Mooy. "Fluorometric Quantification of Polyphosphate in Environmental Plankton Samples: Extraction Protocols, Matrix Effects, and Nucleic Acid Interference." Applied and Environmental Microbiology 79, no. 1 (October 26, 2012): 273–81. http://dx.doi.org/10.1128/aem.02592-12.

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ABSTRACTPolyphosphate (polyP) is a ubiquitous biochemical with many cellular functions and comprises an important environmental phosphorus pool. However, methodological challenges have hampered routine quantification of polyP in environmental samples. We tested 15 protocols to extract inorganic polyphosphate from natural marine samples and cultured cyanobacteria for fluorometric quantification with 4′,6-diamidino-2-phenylindole (DAPI) without prior purification. A combination of brief boiling and digestion with proteinase K was superior to all other protocols, including other enzymatic digestions and neutral or alkaline leaches. However, three successive extractions were required to extract all polyP. Standard addition revealed matrix effects that differed between sample types, causing polyP to be over- or underestimated by up to 50% in the samples tested here. Although previous studies judged that the presence of DNA would not complicate fluorometric quantification of polyP with DAPI, we show that RNA can cause significant interference at the wavelengths used to measure polyP. Importantly, treating samples with DNase and RNase before proteinase K digestion reduced fluorescence by up to 57%. We measured particulate polyP along a North Pacific coastal-to-open ocean transect and show that particulate polyP concentrations increased toward the open ocean. While our final method is optimized for marine particulate matter, different environmental sample types may need to be assessed for matrix effects, extraction efficiency, and nucleic acid interference.

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Connon, Stephanie A., and Stephen J. Giovannoni. "High-Throughput Methods for Culturing Microorganisms in Very-Low-Nutrient Media Yield Diverse New Marine Isolates." Applied and Environmental Microbiology 68, no. 8 (August 2002): 3878–85. http://dx.doi.org/10.1128/aem.68.8.3878-3885.2002.

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ABSTRACT Microbial diversity studies based on the cloning and sequencing of DNA from nature support the conclusion that only a fraction of the microbial diversity is currently represented in culture collections. Out of over 40 known prokaryotic phyla, only half have cultured representatives. In an effort to culture the uncultured phylotypes from oligotrophic marine ecosystems, we developed high-throughput culturing procedures that utilize the concept of extinction culturing to isolate cultures in small volumes of low-nutrient media. In these experiments, marine bacteria were isolated and cultivated at in situ substrate concentrations—typically 3 orders of magnitude less than common laboratory media. Microtiter plates and a newly developed procedure for making cell arrays were employed to raise the throughput rate and lower detection sensitivity, permitting cell enumeration from 200-μl aliquots of cultures with densities as low as 103 cells/ml. Approximately 2,500 extinction cultures from 11 separate samplings of marine bacterioplankton were screened over the course of 3 years. Up to 14% of the cells collected from coastal seawater were cultured by this method, which was 14- to 1,400-fold higher than the numbers obtained by traditional microbiological culturing techniques. Among the microorganisms cultured were four unique cell lineages that belong to previously uncultured or undescribed marine Proteobacteria clades known from environmental gene cloning studies. These cultures are related to the clades SAR11 (α subclass), OM43 (β subclass), SAR92 (γ subclass), and OM60/OM241 (γ subclass). This method proved successful for the cultivation of previously uncultured marine bacterioplankton that have consistently been found in marine clone libraries.

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Piquet, Anouk M. T., Henk Bolhuis, Andrew T. Davidson, Paul G. Thomson, and Anita G. J. Buma. "Diversity and dynamics of Antarctic marine microbial eukaryotes under manipulated environmental UV radiation." FEMS Microbiology Ecology 66, no. 2 (November 2008): 352–66. http://dx.doi.org/10.1111/j.1574-6941.2008.00588.x.

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Gao, Zheng, Binglin Li, Chengchao Zheng, and Guangyi Wang. "Molecular Detection of Fungal Communities in the Hawaiian Marine Sponges Suberites zeteki and Mycale armata." Applied and Environmental Microbiology 74, no. 19 (August 1, 2008): 6091–101. http://dx.doi.org/10.1128/aem.01315-08.

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ABSTRACT Symbiotic microbes play a variety of fundamental roles in the health and habitat ranges of their hosts. While prokaryotes in marine sponges have been broadly characterized, the diversity of sponge-inhabiting fungi has barely been explored using molecular approaches. Fungi are an important component of many marine and terrestrial ecosystems, and they may be an ecologically significant group in sponge-microbe interactions. This study tested the feasibility of using existing fungal primers for molecular analysis of sponge-associated fungal communities. None of the eight selected primer pairs yielded satisfactory results in fungal rRNA gene or internal transcribed spacer (ITS) clone library constructions. However, 3 of 10 denaturing gradient gel electrophoresis (DGGE) primer sets, which were designed to preferentially amplify fungal rRNA gene or ITS regions from terrestrial environmental samples, were successfully amplified from fungal targets in marine sponges. DGGE analysis indicated that fungal communities differ among different sponge species (Suberites zeteki and Mycale armata) and also vary between sponges and seawater. Sequence analysis of DGGE bands identified 23 and 21 fungal species from each of the two sponge species S. zeteki and M. armata, respectively. These species were representatives of 11 taxonomic orders and belonged to the phyla of Ascomycota (seven orders) and Basidiomycota (four orders). Five of these taxonomic orders (Malasseziales, Corticiales, Polyporales, Agaricales, and Dothideomycetes et Chaetothyriomcetes incertae sedis) have now been identified for the first time in marine sponges. Seven and six fungal species from S. zeteki and M. armata, respectively, are potentially new species because of their low sequence identity (≤98%) with their references in GenBank. Phylogenetic analysis indicated sponge-derived sequences were clustered into “marine fungus clades” with those from other marine habitats. This is the first report of molecular analysis of fungal communities in marine sponges, adding depth and dimension to our understanding of sponge-associated microbial communities.

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Joyner, Jessica, David Wanless, Christopher D. Sinigalliano, and Erin K. Lipp. "Use of Quantitative Real-Time PCR for Direct Detection of Serratia marcescens in Marine and Other Aquatic Environments." Applied and Environmental Microbiology 80, no. 5 (December 27, 2013): 1679–83. http://dx.doi.org/10.1128/aem.02755-13.

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ABSTRACTSerratia marcescensis the etiological agent of acroporid serratiosis, a distinct form of white pox disease in the threatened coralAcropora palmata. The pathogen is commonly found in untreated human waste in the Florida Keys, which may contaminate both nearshore and offshore waters. Currently there is no direct method for detection of this bacterium in the aquatic or reef environment, and culture-based techniques may underestimate its abundance in marine waters. A quantitative real-time PCR assay was developed to detectS. marcescensdirectly from environmental samples, including marine water, coral mucus, sponge tissue, and wastewater. The assay targeted theluxSgene and was able to distinguishS. marcescensfrom otherSerratiaspecies with a reliable quantitative limit of detection of 10 cell equivalents (CE) per reaction. The method could routinely discern the presence ofS. marcescensfor as few as 3 CE per reaction, but it could not be reliably quantified at this level. The assay detected environmentalS. marcescensin complex sewage influent samples at up to 761 CE ml−1and in septic system-impacted residential canals in the Florida Keys at up to 4.1 CE ml−1. This detection assay provided rapid quantitative abilities and good sensitivity and specificity, which should offer an important tool for monitoring this ubiquitous pathogen that can potentially impact both human health and coral health.

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Yoshikawa, Kazuhiro, Kyoko Adachi, Miyuki Nishijima, Takahide Takadera, Seiji Tamaki, Ken-ichi Harada, Kenichi Mochida, and Hiroshi Sano. "β-Cyanoalanine Production by Marine Bacteria on Cyanide-Free Medium and Its Specific Inhibitory Activity toward Cyanobacteria." Applied and Environmental Microbiology 66, no. 2 (February 1, 2000): 718–22. http://dx.doi.org/10.1128/aem.66.2.718-722.2000.

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ABSTRACT In screening the culture broth of marine bacteria collected at Yap (Micronesia), Palau (Belau), and Okinawa (the southwest islands of Japan) for antimicroalgal activity, 37 out of 2,594 bacterial isolates tested were found to produce anticyanobacterial substances against Oscillatoria amphibia NIES-361. One strain, C-979, identified as a Vibrio sp., was selected and cultured in 2.4 liters of marine broth 2216 to identify the bioactive compound produced by the strain. The purified very hydrophilic compound (16.4 mg) was determined to be β-cyano-l-alanine (l-CNAla) by instrumental analyses and the application of the advanced Marfey method. l-CNAla did not inhibit the growth of bacteria, yeast, or eukaryotic microalgae, but some cyanobacteria were found to be sensitive to l-CNAla at a concentration of 0.4 to 25 μg/ml. The effect of l-CNAla on some other environmental organisms, including invertebrates and a macroalgae, is discussed. CNAla production in marine broth was examined by thin-layer chromatography for the 37 bacterial isolates which produced an anticyanobacterial substance. The broth of 36 of these strains contained CNAla, suggesting the wide distribution of CNAla production by marine bacteria. This is the first report on bacteria that produce CNAla without a supply of the cyanide ion in the medium.

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White, James R., Patricia Escobar-Paramo, Emmanuel F. Mongodin, Karen E. Nelson, and Jocelyne DiRuggiero. "Extensive Genome Rearrangements and Multiple Horizontal Gene Transfers in a Population of Pyrococcus Isolates from Vulcano Island, Italy." Applied and Environmental Microbiology 74, no. 20 (August 22, 2008): 6447–51. http://dx.doi.org/10.1128/aem.01024-08.

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ABSTRACT The extent of chromosome rearrangements in Pyrococcus isolates from marine hydrothermal vents in Vulcano Island, Italy, was evaluated by high-throughput genomic methods. The results illustrate the dynamic nature of the genomes of the genus Pyrococcus and raise the possibility of a connection between rapidly changing environmental conditions and adaptive genomic properties.

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Grivard, Antoine, Isabelle Goubet, Luiz Miranda de Souza Duarte Filho, Valérie Thiéry, Sylvie Chevalier, Raimundo Gonçalves de Oliveira-Junior, Noureddine El Aouad, et al. "Archaea Carotenoids: Natural Pigments with Unexplored Innovative Potential." Marine Drugs 20, no. 8 (August 17, 2022): 524. http://dx.doi.org/10.3390/md20080524.

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For more than 40 years, marine microorganisms have raised great interest because of their major ecological function and their numerous applications for biotechnology and pharmacology. Particularly, Archaea represent a resource of great potential for the identification of new metabolites because of their adaptation to extreme environmental conditions and their original metabolic pathways, allowing the synthesis of unique biomolecules. Studies on archaeal carotenoids are still relatively scarce and only a few works have focused on their industrial scale production and their biotechnological and pharmacological properties, while the societal demand for these bioactive pigments is growing. This article aims to provide a comprehensive review of the current knowledge on carotenoid metabolism in Archaea and the potential applications of these pigments in biotechnology and medicine. After reviewing the ecology and classification of these microorganisms, as well as their unique cellular and biochemical characteristics, this paper highlights the most recent data concerning carotenoid metabolism in Archaea, the biological properties of these pigments, and biotechnological considerations for their production at industrial scale.

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Zhang, Ruifu, and Ji-Dong Gu. "Complete Sequence of Plasmid pMP1 from the Marine Environmental Vibrio vulnificus and Location of Its Replication Origin." Marine Biotechnology 11, no. 4 (November 14, 2008): 456–62. http://dx.doi.org/10.1007/s10126-008-9160-3.

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Arrieta, Jesús M., and Gerhard J. Herndl. "Assessing the Diversity of Marine Bacterial β-Glucosidases by Capillary Electrophoresis Zymography." Applied and Environmental Microbiology 67, no. 10 (October 1, 2001): 4896–900. http://dx.doi.org/10.1128/aem.67.10.4896-4900.2001.

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ABSTRACT We propose a new method for the fast separation and detection of β-glucosidases in environmental samples. With this approach, β-glucosidases extracted from bacteria are evidenced by substrate-incorporated capillary electrophoresis (CE zymography) and their kinetic parameters can be determined by repeated injections using different substrate concentrations. Preliminary results obtained with natural bacterial communities from the coastal North Sea suggest that the diversity of β-glucosidases in the marine environment might be much higher than previously observed.

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Journal articles on the topic 'Environmental marine biotechnology'

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