Disentangling the effects of sulfate and other seawater ions on microbial communities and greenhouse gas emissions in a coastal forested wetland

ISME Communications, Год журнала: 2024, Номер 4(1)

Опубликована: Янв. 1, 2024

Abstract Seawater intrusion into freshwater wetlands causes changes in microbial communities and biogeochemistry, but the exact mechanisms driving these remain unclear. Here we use a manipulative laboratory microcosm experiment, combined with DNA sequencing biogeochemical measurements, to tease apart effects of sulfate from other seawater ions. We examined taxonomy function as well emissions carbon dioxide, methane, nitrous oxide response ion concentrations. Greenhouse gas richness composition were altered by artificial regardless whether was present, whereas alone did not alter or communities. Surprisingly, addition lead increases abundance reducing bacteria sulfur cycling genes. Similarly, genes involved carbon, nitrogen, phosphorus responded more strongly than sulfate. These results suggest that ions present seawater, sulfate, drive ecological responses may be drivers increased methane soils received addition. A better understanding how different components salt water community is necessary forecast consequences coastal wetland salinization.

Язык: Английский

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Microbial ecology and site characteristics underlie differences in salinity-methane relationships in coastal wetlands

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Апрель 2, 2024

Abstract Methane (CH 4 ) is a potent greenhouse gas emitted by archaea in anaerobic environments such as wetland soils. Tidal freshwater wetlands are predicted to become increasingly saline sea levels rise due climate change. Previous work has shown that increases salinity generally decrease CH emissions, but with considerable variation, including instances where salinization increased flux. We measured microbial community composition, biogeochemistry, and flux from field samples lab experiments four different sites across wide geographic range. sought assess how site differences ecology affect emissions influenced salinization. was generally, not always, positively correlated CO 2 flux, soil carbon, ammonium, phosphate, pH. Methanogen guilds were all sites, while methanotroph both negatively depending on site. There mixed support for negative relationships between fluxes concentrations of alternative electron acceptors abundances taxa reduce them. /salinity ranged negative, neutral, positive appeared be characteristics pH plant which also likely contributed communities. The activity site-specific microbes may respond differently low-level an important driver relationships. Our results suggest several factors make it difficult generalize highlight the need paired measurements broader range sites.

Язык: Английский

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Methane Emissions From Seabed to Atmosphere in Polar Oceans Revealed by Direct Methane Flux Measurements

Journal of Geophysical Research Atmospheres, Год журнала: 2024, Номер 129(14)

Опубликована: Июль 26, 2024

Abstract Sea‐air methane flux was measured directly by the eddy‐covariance method across approximately 60,000 km of Arctic and Antarctic cruises during a number summers. The Ocean (north 60°N, between 20°W 50°E) Southern (south 50°S, 70°W 30°E) are found to be on‐shelf sources atmospheric with mean sea‐air fluxes 9.17 ± 2.91 (SEM (standard error mean)) μmol m −2 d −1 8.98 0.91 , respectively. Off‐shelf, this region is source (mean 2.39 0.68 ), while sink −0.77 0.37 ). highest observed around west Svalbard, South Georgia, Shetland Islands Bransfield Strait; areas evidence presence flares emanating from seabed. Hence, study may provide direct emission seabed atmosphere in both Antarctic. Comparing previous studies, results indicate an increase seafloor seepage over timescales several decades. As climate change exacerbates rising water temperatures, continued monitoring release polar oceans into future crucial.

Язык: Английский

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Decomposing a San Francisco estuary microbiome using long-read metagenomics reveals species- and strain-level dominance from picoeukaryotes to viruses

mSystems, Год журнала: 2024, Номер 9(9)

Опубликована: Авг. 19, 2024

Although long-read sequencing has enabled obtaining high-quality and complete genomes from metagenomes, many challenges still remain to completely decompose a metagenome into its constituent prokaryotic viral genomes. This study focuses on decomposing an estuarine obtain more accurate estimate of microbial diversity. To achieve this, we developed new bead-based DNA extraction method, novel bin refinement obtained 150 Gbp Nanopore sequencing. We that there are ~500 bacterial archaeal species in our sample 68 bins (>90% complete, <5% contamination, ≤5 contigs, contig length >100 kbp, all ribosomal tRNA genes). also contigs picoeukaryotes, environmental larger eukaryotes such as mammals, mitochondrial chloroplast detected ~40,000 populations. Our analysis indicates only few strains comprise most the abundances.

Язык: Английский

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Automated annotation of scientific texts for ML-based keyphrase extraction and validation

Database, Год журнала: 2024, Номер 2024

Опубликована: Янв. 1, 2024

Abstract Advanced omics technologies and facilities generate a wealth of valuable data daily; however, the often lack essential metadata required for researchers to find, curate, search them effectively. The poses significant challenge in utilization these sets. Machine learning (ML)–based extraction techniques have emerged as potentially viable approach automatically annotating scientific sets with necessary enabling effective search. Text labeling, usually performed manually, plays crucial role validating machine-extracted metadata. However, manual labeling is time-consuming not always feasible; thus, there need develop automated text order accelerate process innovation. This particularly urgent fields such environmental genomics microbiome science, which historically received less attention terms curation creation gold-standard mining In this paper, we present two novel approaches validation ML-generated unlabeled texts, specific applications genomics. Our show potential new ways leverage existing information that only available select documents within corpus validate ML models, can then be used describe remaining corpus. first technique exploits relationships between different types sources related same research study, publications proposals. second takes advantage domain-specific controlled vocabularies or ontologies. detail applying context validation. results proposed label assignment both generic highly labels up 44% matching those suggested by keyword algorithm.

Язык: Английский

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Alternating Conditional Expectations: Introducing a Non‐Parametric Statistical Method to Interpret Long‐Term Greenhouse Gas Flux Measurements Over Semi‐Arid and Wetland Ecosystems

Journal of Geophysical Research Biogeosciences, Год журнала: 2024, Номер 129(3)

Опубликована: Фев. 26, 2024

Abstract We explore the potential of using a non‐parametric statistical method called Alternating Conditional Expectations, ACE, to quantify functional relationships in biogeosciences. Here, ACE is used non‐linear and multi‐faceted responses greenhouse gas fluxes set biophysical forcings, when shapes those response surfaces are unknown. evaluated over two contrasting ecosystems time steps. One case involved quantifying controls water vapor carbon dioxide (CO 2 ) semi‐arid oak savanna daily integrated fluxes. The other CO methane (CH 4 flux measurements forcings at restored tidal wetland thirty‐minute averages. model, based on independent variables, explained up 90% variation densities net exchange site. This fit was defined by distinct such drivers as gross primary production, photosynthetically active radiation, air temperature, pressure deficit soil moisture. At site, we with short‐term capture influence rising falling tides seasonality biological activity. model shape forcing due roles exudates, table depth, oxygen level column, temperature vegetation status. fits were less precise than case. fetch varies run‐to‐run basis it comprised heterogeneous mosaic open vegetation. Furthermore, difficult monitor environmental conditions archaea bacteria sediments that produce dioxide.

Язык: Английский

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WITHDRAWN: Contrasting effects of symbiont inoculation on soil microbiota functionalities in a rehabilitation programme of salt-affected lands

Research Square (Research Square), Год журнала: 2024, Номер unknown

Опубликована: Авг. 29, 2024

The full text of this preprint has been withdrawn by the authors while they make corrections to work. Therefore, do not wish work be cited as a reference. Questions should directed corresponding author.

Язык: Английский

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Contrasting effects of symbiont inoculation on soil microbiota functionalities in a rehabilitation programme of salt-affected lands

Research Square (Research Square), Год журнала: 2024, Номер unknown

Опубликована: Сен. 26, 2024

Soil salinization has become a major global ecosystem sustainability issue. In Senegal, promising restoration of salt-affected lands been achieved by the implementation ecological engineering strategies based on beneficial associations between Casuarina species and salt-tolerant symbiotic microorganisms. However, extent impacts symbiont inoculants native soil microbiota and, consequently, functioning is fragmentary. The current study aimed to evaluate changes in associated with use inoculant mixed Casuarinaceae plantations lands. Symbiont inoculation led decrease diversity fungi but not bacteria. whole structure was impacted inoculation, as case for salinity Casuarina species. species also dominant taxa constituting microbiota, only affected bacterial diversity. Important modifications functionalities were revealed, notably, abundance pathogens related an increase fungal increasing salinity. nutrient cycling, mostly micronutrient cycling N fixation, main factors affecting soil.

Язык: Английский

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When and where can coastal wetland restoration increase carbon sequestration as a natural climate solution?

Cambridge Prisms Coastal Futures, Год журнала: 2024, Номер 2

Опубликована: Янв. 1, 2024

Abstract Coastal wetlands are hotspots of carbon sequestration, and their conservation restoration can help to mitigate climate change. However, there remains uncertainty on when where coastal wetland most effectively act as natural solutions (NCS). Here, we synthesize current understanding illustrate the requirements for benefit climate, discuss potential paths forward that address key uncertainties impeding implementation. To be effective NCS, projects will accrue cooling benefits would not occur without management action (additionality), implementable (feasibility) persist over management-relevant timeframes (permanence). Several issues add if these minimum met. First, serve both a landscape source sink other habitats, increasing in additionality. Second, potentially migrate outside project footprints they respond sea-level rise, permanence. first two issues, system-wide approach may necessary, rather than basing only changes within boundaries. Third, need NCS function decadal timescales means methane responses necessary include planning monitoring. Finally, is how much data required justify action. We summarize make binary decision whether net from action, noting more readily available quantify magnitude crediting purposes. By reducing uncertainty, implemented at scale significantly contribute addressing crisis.

Язык: Английский

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Contrasting effects of symbiont inoculation on soil microbiota functionalities in a rehabilitation programme of salt-affected lands

Research Square (Research Square), Год журнала: 2024, Номер unknown

Опубликована: Авг. 26, 2024

Soil salinization has become a major global ecosystem sustainability issue. In Senegal, promising restoration of salt-affected lands been achieved by the implementation ecological engineering strategies based on beneficial associations between Casuarina species and salt-tolerant symbiotic microorganisms. However, extent impacts symbiont inoculants native soil microbiota and, consequently, functioning is fragmentary. The current study aimed to evaluate changes in associated with use inoculant mixed Casuarinaceae plantations lands. Symbiont inoculation led decrease diversity fungi but not bacteria. whole structure was impacted inoculation, as case for salinity species. also dominant taxa constituting microbiota, only affected bacterial diversity. Important modifications functionalities were revealed, notably, abundance pathogens related an increase fungal increasing salinity. nutrient cycling, mostly micronutrient cycling N fixation, main factors affecting soil.

Язык: Английский

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