Environmental DNA

Oxford University Press eBooks, Journal Year: 2018, Volume and Issue: unknown

Published: Feb. 15, 2018

Abstract Environmental DNA (eDNA), i.e. released in the environment by any living form, represents a formidable opportunity to gather high-throughput and standard information on distribution or feeding habits of species. It has therefore great potential for applications ecology biodiversity management. However, this research field is fast-moving, involves different areas expertise currently lacks approaches, which calls an up-to-date comprehensive synthesis. monitoring covers current methods based eDNA, with particular focus “eDNA metabarcoding”. Intended scientists managers, it provides background allow design sound experiments. revisits all steps necessary produce high-quality metabarcoding data such as sampling, metabarcode design, optimization PCR sequencing protocols, well analysis large datasets. All these are presented discussing challenges eDNA-based approaches infer parameters ecological processes. The last chapters book review how been used so far unravel novel patterns diversity space time, detect species, answer new questions various ecosystems organisms. constitutes essential reading graduate students, researchers practitioners who do not have strong molecular genetics willing use eDNA biomonitoring.

Language: Английский

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Methane Feedbacks to the Global Climate System in a Warmer World

Reviews of Geophysics, Journal Year: 2018, Volume and Issue: 56(1), P. 207 - 250

Published: Feb. 16, 2018

Abstract Methane (CH 4 ) is produced in many natural systems that are vulnerable to change under a warming climate, yet current CH budgets, as well future shifts emissions, have high uncertainties. Climate has the potential increase emissions from critical such wetlands, marine and freshwater systems, permafrost, methane hydrates, through temperature, hydrology, vegetation, landscape disturbance, sea level rise. Increased these would turn induce further climate change, resulting positive feedback. Here we synthesize biological, geochemical, physically focused feedback literature, bringing together key findings of disciplines. We discuss environment‐specific processes, including microbial, physical, geochemical interlinkages timescales on which they operate, present state knowledge feedbacks immediate distant future. The important linkages between microbial activity discussed with aim better constrain sensitivity cycle predictions. determine wetlands will form majority up 2100. Beyond this timescale, permafrost environments could become more important. Significant atmosphere dissociation hydrates not expected near Our highlight importance quantifying whether consumption can counterbalance production scenarios.

Language: Английский

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Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments

Nature Communications, Journal Year: 2018, Volume and Issue: 9(1)

Published: Nov. 21, 2018

Microbes in Guaymas Basin (Gulf of California) hydrothermal sediments thrive on hydrocarbons and sulfur experience steep, fluctuating temperature chemical gradients. The functional capacities communities inhabiting this dynamic habitat are largely unknown. Here, we reconstructed 551 genomes from hydrothermally influenced, nearby cold belonging to 56 phyla (40 uncultured). These comprise 22 unique lineages, including five new candidate phyla. In contrast findings hydrocarbon seeps, hydrothermal-associated more diverse archaea dominate over bacteria. Genome-based metabolic inferences provide first insights into the ecological niches these uncultured microbes, methane cycling Crenarchaeota alkane utilization ANME-1. shaped by a high biodiversity, partitioning among nitrogen pathways redundancy core carbon-processing pathways. select for distinctive microbial that stand out expansive open up physiological perspectives ecosystem function.

Language: Английский

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Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments

The ISME Journal, Journal Year: 2016, Volume and Issue: 10(8), P. 1939 - 1953

Published: Feb. 12, 2016

Language: Английский

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A Metagenomics-Based Metabolic Model of Nitrate-Dependent Anaerobic Oxidation of Methane by Methanoperedens-Like Archaea

Frontiers in Microbiology, Journal Year: 2015, Volume and Issue: 6

Published: Dec. 18, 2015

Methane oxidation is an important process to mitigate the emission of greenhouse gas methane and further exacerbating climate forcing. Both aerobic anaerobic microorganisms have been reported catalyze with only a few possible electron acceptors. Recently, new were identified that could couple nitrate or nitrite reduction. Here we investigated such enrichment culture at (meta)genomic level establish metabolic model nitrate-driven (nitrate-AOM). Nitrate-AOM catalyzed by archaeon closely related (reverse) methanogens belongs ANME-2d clade, tentatively named Methanoperedens nitroreducens. may be activated methyl-CoM reductase subsequently undergo full carbon dioxide via reverse methanogenesis. All enzymes this pathway present expressed in culture. The genome archaeal encoded variety involved transport chain similar those found Methanosarcina species additional features not previously methane-converting archaea. Nitrate reduction seems located pseudoperiplasm unusual Nar-like protein complex. A small part resulting reduced ammonium which Nrf-type reductase. One key questions how electrons from cytoplasmically methanogenesis reach pseudoperiplasm. Electron M. nitroreducens probably involves cofactor F420 cytoplasm, quinones cytoplasmic membrane cytochrome c membrane-bound includes F420H2 dehydrogenase Rieske/cytochrome b Based on transcriptome studies tentative central energy metabolism nitrate-AOM work presented discussed.

Language: Английский

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Growth of sedimentaryBathyarchaeotaon lignin as an energy source

Proceedings of the National Academy of Sciences, Journal Year: 2018, Volume and Issue: 115(23), P. 6022 - 6027

Published: May 17, 2018

Members of the archaeal phylum Bathyarchaeota are among most abundant microorganisms on Earth. Although versatile metabolic capabilities such as acetogenesis, methanogenesis, and fermentation have been suggested for bathyarchaeotal members, no direct confirmation these functions has achieved through growth in laboratory. Here we demonstrate, basis gene-copy numbers probing lipids, subgroup Bathy-8 enrichments estuarine sediments with biopolymer lignin. Other organic substrates (casein, oleic acid, cellulose, phenol) did not significantly stimulate Meanwhile, putative tetraether lipids incorporated 13C from 13C-bicarbonate only when added concert Our results consistent organoautotrophic a group lignin an energy source bicarbonate carbon shed light into cycling one Earth's biopolymers anoxic marine sediment.

Language: Английский

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Diversity and composition of soil Acidobacteria and Proteobacteria communities as a bacterial indicator of past land-use change from forest to farmland

The Science of The Total Environment, Journal Year: 2021, Volume and Issue: 797, P. 148944 - 148944

Published: July 16, 2021

Language: Английский

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Visualizing in situ translational activity for identifying and sorting slow-growing archaeal−bacterial consortia

Proceedings of the National Academy of Sciences, Journal Year: 2016, Volume and Issue: 113(28)

Published: June 28, 2016

To understand the biogeochemical roles of microorganisms in environment, it is important to determine when and under which conditions they are metabolically active. Bioorthogonal noncanonical amino acid tagging (BONCAT) can reveal active cells by tracking incorporation synthetic acids into newly synthesized proteins. The phylogenetic identity translationally be determined combining BONCAT with rRNA-targeted fluorescence situ hybridization (BONCAT-FISH). In theory, BONCAT-labeled could isolated fluorescence-activated cell sorting (BONCAT-FACS) for subsequent genetic analyses. Here, first application, our knowledge, BONCAT-FISH BONCAT-FACS within an environmental context, we probe translational activity microbial consortia catalyzing anaerobic oxidation methane (AOM), a dominant sink ocean. These consortia, typically composed methane-oxidizing archaea (ANME) sulfate-reducing bacteria, have been difficult study due their slow growth rates, fundamental questions remain about ecology diversity interactions occurring between ANME associated partners. Our activity-correlated analyses >16,400 aggregates provide evidence, that AOM affiliated all five major clades concurrently controlled conditions. Surprisingly, individual followed whole-genome amplification 16S rRNA gene sequencing revealed previously unrecognized members poorly understood phylum Verrucomicrobia This finding, together observation ANME-associated found variety geographically distinct seep environments, suggests broader range symbiotic relationships than thought.

Language: Английский

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Lanthanide-dependent cross-feeding of methane-derived carbon is linked by microbial community interactions

Proceedings of the National Academy of Sciences, Journal Year: 2016, Volume and Issue: 114(2), P. 358 - 363

Published: Dec. 27, 2016

The utilization of methane, a potent greenhouse gas, is an important component local and global carbon cycles that characterized by tight linkages between methane-utilizing (methanotrophic) nonmethanotrophic bacteria. It has been suggested the methanotroph sustains these nonmethanotrophs cross-feeding, because subsequent products methane oxidation pathway, such as methanol, represent alternative sources. We established cocultures in microcosm model system to determine mechanism substrate underlay observed cross-feeding environment. Lanthanum, rare earth element, was applied its increasing importance methylotrophy. used co-occurring strains isolated from Lake Washington sediment are involved utilization: two methylotrophs. Gene-expression profiles mutant analyses suggest methanol dominant energy source provides support growth nonmethanotrophs. However, presence nonmethanotroph, gene expression dehydrogenase (MDH) shifts lanthanide-dependent MDH (XoxF)-type, calcium-dependent (MxaF)-type. Correspondingly, released into medium only when expresses MxaF-type MDH. These results which partner induces change MDHs, resulting release for growth. This partner-induced benefits paradigm microbial interactions cannot be studies pure cultures, underscoring synthetic community approaches understand environmental microbiomes.

Language: Английский

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Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity

The ISME Journal, Journal Year: 2021, Volume and Issue: 15(8), P. 2366 - 2378

Published: March 1, 2021

Abstract In marine ecosystems, viruses exert control on the composition and metabolism of microbial communities, influencing overall biogeochemical cycling. Deep sea sediments associated with cold seeps are known to host taxonomically diverse but little is about infecting these microorganisms. Here, we probed metagenomes from seven geographically across global oceans assess viral diversity, virus–host interaction, virus-encoded auxiliary metabolic genes (AMGs). Gene-sharing network comparisons inhabiting other ecosystems reveal that seep harbour considerable unexplored diversity. Most display high degrees endemism fluid flux being one main drivers community composition. silico predictions linked 14.2% populations many belonging poorly understood candidate bacterial archaeal phyla. Lysis was predicted be a predominant lifestyle based lineage-specific virus/host abundance ratios. Metabolic prokaryotic genomes AMGs suggest influence hydrocarbon biodegradation at seeps, as well carbon, sulfur nitrogen cycling via virus-induced mortality and/or augmentation. Overall, findings diversity biogeography indicate how may manipulate ecology biogeochemistry.

Language: Английский

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