scholarly journals Microbial drivers of methane emissions from unrestored industrial salt ponds

2021 ◽  
Author(s):  
Jinglie Zhou ◽  
Susanna M. Theroux ◽  
Clifton P. Bueno de Mesquita ◽  
Wyatt H. Hartman ◽  
Ye Tian ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Methane Flux ◽  
Methane Emissions ◽  
Metagenomic Data ◽  
Rrna Gene ◽  
Salt Ponds ◽  
Salt Pond ◽  
Reference Wetlands ◽  
Reference Wetland ◽  
The Impact

AbstractWetlands are important carbon (C) sinks, yet many have been destroyed and converted to other uses over the past few centuries, including industrial salt making. A renewed focus on wetland ecosystem services (e.g., flood control, and habitat) has resulted in numerous restoration efforts whose effect on microbial communities is largely unexplored. We investigated the impact of restoration on microbial community composition, metabolic functional potential, and methane flux by analyzing sediment cores from two unrestored former industrial salt ponds, a restored former industrial salt pond, and a reference wetland. We observed elevated methane emissions from unrestored salt ponds compared to the restored and reference wetlands, which was positively correlated with salinity and sulfate across all samples. 16S rRNA gene amplicon and shotgun metagenomic data revealed that the restored salt pond harbored communities more phylogenetically and functionally similar to the reference wetland than to unrestored ponds. Archaeal methanogenesis genes were positively correlated with methane flux, as were genes encoding enzymes for bacterial methylphosphonate degradation, suggesting methane is generated both from bacterial methylphosphonate degradation and archaeal methanogenesis in these sites. These observations demonstrate that restoration effectively converted industrial salt pond microbial communities back to compositions more similar to reference wetlands and lowered salinities, sulfate concentrations, and methane emissions.

scholarly journals Shaping of the Present-Day Deep Biosphere at Chicxulub by the Impact Catastrophe That Ended the Cretaceous

2021 ◽  
Vol 12 ◽  
Author(s):  
Charles S. Cockell ◽  
Bettina Schaefer ◽  
Cornelia Wuchter ◽  
Marco J. L. Coolen ◽  
Kliti Grice ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Amplicon Sequencing ◽  
Granitic Rocks ◽  
Rrna Gene ◽  
Deep Biosphere ◽  
Deep Subsurface ◽  
Cell Biomass ◽  
Colonization Potential ◽  
The Impact

We report on the effect of the end-Cretaceous impact event on the present-day deep microbial biosphere at the impact site. IODP-ICDP Expedition 364 drilled into the peak ring of the Chicxulub crater, México, allowing us to investigate the microbial communities within this structure. Increased cell biomass was found in the impact suevite, which was deposited within the first few hours of the Cenozoic, demonstrating that the impact produced a new lithological horizon that caused a long-term improvement in deep subsurface colonization potential. In the biologically impoverished granitic rocks, we observed increased cell abundances at impact-induced geological interfaces, that can be attributed to the nutritionally diverse substrates and/or elevated fluid flow. 16S rRNA gene amplicon sequencing revealed taxonomically distinct microbial communities in each crater lithology. These observations show that the impact caused geological deformation that continues to shape the deep subsurface biosphere at Chicxulub in the present day.

Water management and phenology influence the root-associated rice field microbiota

2020 ◽  
Vol 96 (9) ◽  
Author(s):  
Matteo Chialva ◽  
Stefano Ghignone ◽  
Paolo Cozzi ◽  
Barbara Lazzari ◽  
Paola Bonfante ◽  
...  
Keyword(s):  
Water Management ◽  
Microbial Communities ◽  
Rice Field ◽  
Water Status ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Upland Conditions ◽  
The Impact ◽  
Comprehensive Study

ABSTRACT Microbial communities associated with plants are greatly influenced by water availability in soil. In flooded crops, such as rice, the impact of water management on microbial dynamics is not fully understood. Here, we present a comprehensive study of the rice microbiota investigated in an experimental field located in one of the most productive areas of northern Italy. The microbiota associated with paddy soil and root was investigated using 454 pyrosequencing of 16S, ITS and 18S rRNA gene amplicons under two different water managements, upland (non-flooded, aerobic) and lowland (traditional flooding, anaerobic), at three plant development stages. Results highlighted a major role of the soil water status in shaping microbial communities, while phenological stage had low impacts. Compositional shifts in prokaryotic and fungal communities upon water management consisted in significant abundance changes of Firmicutes, Methanobacteria, Chloroflexi, Sordariomycetes, Dothideomycetes and Glomeromycotina. A vicariance in plant beneficial microbes and between saprotrophs and pathotrophs was observed between lowland and upland. Moreover, through network analysis, we demonstrated different co-abundance dynamics between lowland and upland conditions with a major impact on microbial hubs (strongly interconnected microbes) that fully shifted to aerobic microbes in the absence of flooding.

scholarly journals Quantifying the impact of emission outbursts and non-stationary flow on eddy-covariance CH<sub>4</sub> flux measurements using wavelet techniques

2019 ◽  
Vol 16 (16) ◽  
pp. 3113-3131 ◽  
Author(s):  
Mathias Göckede ◽  
Fanny Kittler ◽  
Carsten Schaller
Keyword(s):  
Eddy Covariance ◽  
Methane Flux ◽  
Stationary Flow ◽  
Methane Emissions ◽  
Gap Filling ◽  
Short Term ◽  
Flux Measurements ◽  
Systematic Biases ◽  
The Impact ◽  
Short Term Variability

Abstract. Methane flux measurements by the eddy-covariance technique are subject to large uncertainties, particularly linked to the partly highly intermittent nature of methane emissions. Outbursts of high methane emissions, termed event fluxes, hold the potential to introduce systematic biases into derived methane budgets, since under such conditions the assumption of stationarity of the flow is violated. In this study, we investigate the net impact of this effect by comparing eddy-covariance fluxes against a wavelet-derived reference that is not negatively influenced by non-stationarity. Our results demonstrate that methane emission events influenced 3 %–4 % of the flux measurements and did not lead to systematic biases in methane budgets for the analyzed summer season; however, the presence of events substantially increased uncertainties in short-term flux rates. The wavelet results provided an excellent reference to evaluate the performance of three different gap-filling approaches for eddy-covariance methane fluxes, and we show that none of them could reproduce the range of observed flux rates. The integrated performance of the gap-filling methods for the longer-term dataset varied between the two eddy-covariance towers involved in this study, and we show that gap-filling remains a large source of uncertainty linked to limited insights into the mechanisms governing the short-term variability in methane emissions. With the capability for broadening our observational methane flux database to a wider range of conditions, including the direct resolution of short-term variability on the order of minutes, wavelet-derived fluxes hold the potential to generate new insight into methane exchange processes with the atmosphere and therefore also improve our understanding of the underlying processes.

scholarly journals Quantitative Metagenomic Analyses Based on Average Genome Size Normalization

2011 ◽  
Vol 77 (7) ◽  
pp. 2513-2521 ◽  
Author(s):  
Jeremy A. Frank ◽  
Søren J. Sørensen
Keyword(s):  
Microbial Communities ◽  
Genome Size ◽  
Metagenomic Data ◽  
Gene Copy ◽  
Rrna Gene ◽  
Sequence Information ◽  
Ssu Rrna ◽  
Community Members ◽  
Ssu Rrna Gene ◽  
Photosynthetic Carbon

ABSTRACTOver the past quarter-century, microbiologists have used DNA sequence information to aid in the characterization of microbial communities. During the last decade, this has expanded from single genes to microbial community genomics, or metagenomics, in which the gene content of an environment can provide not just a census of the community members but direct information on metabolic capabilities and potential interactions among community members. Here we introduce a method for the quantitative characterization and comparison of microbial communities based on the normalization of metagenomic data by estimating average genome sizes. This normalization can relieve comparative biases introduced by differences in community structure, number of sequencing reads, and sequencing read lengths between different metagenomes. We demonstrate the utility of this approach by comparing metagenomes from two different marine sources using both conventional small-subunit (SSU) rRNA gene analyses and our quantitative method to calculate the proportion of genomes in each sample that are capable of a particular metabolic trait. With both environments, to determine what proportion of each community they make up and how differences in environment affect their abundances, we characterize three different types of autotrophic organisms: aerobic, photosynthetic carbon fixers (theCyanobacteria); anaerobic, photosynthetic carbon fixers (theChlorobi); and anaerobic, nonphotosynthetic carbon fixers (theDesulfobacteraceae). These analyses demonstrate how genome proportionality compares to SSU rRNA gene relative abundance and how factors such as average genome size and SSU rRNA gene copy number affect sampling probability and therefore both types of community analysis.

scholarly journals Alteration of Soil Rhizosphere Communities following Genetic Transformation of White Spruce

2007 ◽  
Vol 73 (13) ◽  
pp. 4128-4134 ◽  
Author(s):  
Philippe M. LeBlanc ◽  
Richard C. Hamelin ◽  
Martin Filion
Keyword(s):  
Genetic Transformation ◽  
Microbial Communities ◽  
Genetic Marker ◽  
Genetically Modified ◽  
Ecological Impact ◽  
White Spruce ◽  
Marker Genes ◽  
Rrna Gene ◽  
Significant Difference ◽  
The Impact

ABSTRACT The application of plant genetic manipulations to agriculture and forestry with the aim of alleviating insect damage through Bacillus thuringiensis transformation could lead to a significant reduction in the release of pesticides into the environment. However, many groups have come forward with very valid and important questions related to potentially adverse effects, and it is crucial to assess and better understand the impact that this technology might have on ecosystems. In this study, we analyzed rhizosphere soil samples collected from the first B. thuringiensis-transformed trees [with insertion of the CryIA(b) toxin-encoding gene] grown in Canada (Val-Cartier, QC, Canada) as part of an ecological impact assessment project. Using a robust amplified rRNA gene restriction analysis approach coupled with 16S rRNA gene sequencing, the rhizosphere-inhabiting microbial communities of white spruce (Picea glauca) genetically modified by biolistic insertion of the cryIA(b), uidA (beta-glucuronidase), and nptII genes were compared with the microbial communities associated with non-genetically modified counterparts and with trees in which only the genetic marker genes uidA and nptII have been inserted. Analysis of 1,728 rhizosphere bacterial clones (576 clones per treatment) using a Cramér-von Mises statistic analysis combined with a Monte Carlo comparison clearly indicated that there was a statistically significant difference (P < 0.05) between the microbial communities inhabiting the rhizospheres of trees carrying the cryIA(b), uidA, and nptII transgenes, trees carrying only the uidA and nptII transgenes, and control trees. Clear rhizosphere microbial community alterations due to B. thuringiensis tree genetic modification have to our knowledge never been described previously and open the door to interesting questions related to B. thuringiensis genetic transformation and also to the impact of commonly used uidA and nptII genetic marker genes.

scholarly journals Microbial Community Structure and Composition is Associated With Host Species and Sex in Sigmodon Cotton Rats

2020 ◽  
Author(s):  
Britton Strickland ◽  
Mira Patel ◽  
Meghan H. Shilts ◽  
Helen H. Boone ◽  
Arash Kamali ◽  
...  
Keyword(s):  
Animal Model ◽  
Microbial Communities ◽  
Viral Infections ◽  
Therapeutic Potential ◽  
Small Animal ◽  
Rrna Gene ◽  
Small Animal Model ◽  
Cotton Rat ◽  
Cotton Rats ◽  
The Impact

Abstract Background: The cotton rat (genus Sigmodon) is an essential small animal model for the study of human infectious disease and viral therapeutic development. However, the impact of the host microbiome on infection outcomes has not been explored in this model, partly due to the lack of a comprehensive characterization of microbial communities across different cotton rat species. Understanding the dynamics of their microbiome could significantly help to better understand its role during when modeling viral infections in this small animal model.Results: We examined the bacterial communities of the gut and three external sites (skin, ear, and nose) of two inbred species of cotton rats commonly used in research (S. hispidus and S. fulviventer) by using 16S rRNA gene sequencing, constituting the first comprehensive catalog of the cotton rat microbiome. We showed that S. fulviventer maintained higher alpha diversity and richness than S. hispidus at external sites (skin, ear, nose), but there were no differentially abundant genera. However, S. fulviventer and S. hispidus had distinct fecal microbiomes composed of several significantly differentially abundant genera. Whole metagenomic shotgun sequencing of fecal samples identified species-level differences between S. hispidus and S. fulviventer, as well as different metabolic pathway functions as a result of differential host microbiome contributions. Furthermore, the microbiome composition of the external sites showed significant sex-based differences while fecal communities were not largely different. Conclusions: Our study shows that host genetic background potentially exerts homeostatic pressures, resulting in distinct microbiomes for two different inbred cotton rat species. Because of the numerous studies that have uncovered strong relationships between host microbiome, viral infection outcomes, and immune responses, our findings represent a strong contribution for understanding the impact of different microbial communities on viral pathogenesis. Furthermore, we provide novel cotton rat microbiome data as a springboard to uncover the full therapeutic potential of the microbiome against viral infections.

Bushfire impacts on a threatened swamp ecosystem: responses of the soil microbial communities and restoration

2021 ◽  
Author(s):  
Nathali Machado de Lima ◽  
Alexandria Thomsen ◽  
Mark Ooi ◽  
Miriam Muñoz-Rojas
Keyword(s):  
Microbial Communities ◽  
Longwall Mining ◽  
Soil Microbial Communities ◽  
Environmental Indicators ◽  
Fire Season ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Drought Period ◽  
Soil Microbial ◽  
The Impact

&lt;p&gt;Australia faced the most extreme and prolonged fire season in 2019-2020, resulting in tragic habitat loss for many threatened species and the destruction of many ecological communities. &amp;#160;Newnes Plateau Shrub Swamps are peatlands located in the upper Blue Mountains region of New South Wales, Australia. These ecosystems perform many important ecological functions while absorbing and filtering water and releasing it slowly back to the environment. Their functions are related to the control of peak flow events, water purification and the harboring of many threatened plant and animal species. Despite their ecological importance, the area has been intensively degraded through longwall mining processes, resulting in the lowering and loss of water tables in the area. In December 2019 these impacts were compounded by an intense prolonged drought period and extensive wildfire. While the effects of these combined factors on the vegetation have been analysed and revealed remarkable negative impacts in the swamps under mining pressures, the effects on the soil microbial communities and related soil functions have not yet been studied. To investigate both drivers (fire and mining activities), we selected three mined swamps and three unmined swamps to assess their soil microbial composition and diversity through Next Generation Sequencing, and to characterise the soil chemical composition. At each site, we collected samples considering three treatments, one in the swamp valley fill and two at two different heights of the swamp valley margin, focusing on the soil close to specific groups of plants (e.g. sedges and shrubs). For each site and treatment, three soil samples (~ 10 m from each other) of 10x10 cm and ~ 3 to 5 cm of depth were collected using a trowel. We aim to build 16S rRNA gene libraries and co-relate them with the soil chemical variables, to assess the impact on these microbial communities and their possible use as environmental indicators and basis for future applied initiatives in conservation and restoration.&lt;/p&gt;&lt;p&gt;&amp;#160;&lt;/p&gt;

scholarly journals Host-specific symbioses and the microbial prey of a pelagic tunicate (Pyrosoma atlanticum)

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Anne W. Thompson ◽  
Anna C. Ward ◽  
Carey P. Sweeney ◽  
Kelly R. Sutherland
Keyword(s):  
Microbial Communities ◽  
Food Webs ◽  
Rrna Gene ◽  
Marine Microorganisms ◽  
Marine Animals ◽  
California Current System ◽  
Marine Food Webs ◽  
Marine Food ◽  
Marine Microbial Communities ◽  
The Impact

AbstractPyrosomes are widely distributed pelagic tunicates that have the potential to reshape marine food webs when they bloom. However, their grazing preferences and interactions with the background microbial community are poorly understood. This is the first study of the marine microorganisms associated with pyrosomes undertaken to improve the understanding of pyrosome biology, the impact of pyrosome blooms on marine microbial systems, and microbial symbioses with marine animals. The diversity, relative abundance, and taxonomy of pyrosome-associated microorganisms were compared to seawater during a Pyrosoma atlanticum bloom in the Northern California Current System using high-throughput sequencing of the 16S rRNA gene, microscopy, and flow cytometry. We found that pyrosomes harbor a microbiome distinct from the surrounding seawater, which was dominated by a few novel taxa. In addition to the dominant taxa, numerous more rare pyrosome-specific microbial taxa were recovered. Multiple bioluminescent taxa were present in pyrosomes, which may be a source of the iconic pyrosome luminescence. We also discovered free-living marine microorganisms in association with pyrosomes, suggesting that pyrosome feeding impacts all microbial size classes but preferentially removes larger eukaryotic taxa. This study demonstrates that microbial symbionts and microbial prey are central to pyrosome biology. In addition to pyrosome impacts on higher trophic level marine food webs, the work suggests that pyrosomes also alter marine food webs at the microbial level through feeding and seeding of the marine microbial communities with their symbionts. Future efforts to predict pyrosome blooms, and account for their ecosystem impacts, should consider pyrosome interactions with marine microbial communities.

scholarly journals Breeding farm, level of feeding and presence of antibiotics in the feed influence rabbit cecal microbiota

2020 ◽  
Vol 2 (1) ◽  
Author(s):  
María Velasco-Galilea ◽  
Miriam Guivernau ◽  
Miriam Piles ◽  
Marc Viñas ◽  
Oriol Rafel ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Management Practices ◽  
Alpha Diversity ◽  
Rrna Gene ◽  
Animal Performance ◽  
Production Environment ◽  
Feed Composition ◽  
Cecal Microbiota ◽  
Relative Abundances ◽  
The Impact

Abstract Background The effect of the production environment and different management practices in rabbit cecal microbiota remains poorly understood. While previous studies have proved the impact of the age or the feed composition, research in the breeding farm and other animal management aspects, such as the presence of antibiotics in the feed or the level of feeding, is still needed. Characterization of microbial diversity and composition of growing rabbits raised under different conditions could help better understand the role these practices play in cecal microbial communities and how it may result in different animal performance. Results Four hundred twenty-five meat rabbits raised in two different facilities, fed under two feeding regimes (ad libitum or restricted) with feed supplemented or free of antibiotics, were selected for this study. A 16S rRNA gene-based assessment through the MiSeq Illumina sequencing platform was performed on cecal samples collected from these individuals at slaughter. Different univariate and multivariate approaches were conducted to unravel the influence of the different factors on microbial alpha diversity and composition at phylum, genus and OTU taxonomic levels. The animals raised in the facility harboring the most stable environmental conditions had greater, and less variable, microbial richness and diversity. Bootstrap univariate analyses of variance and sparse partial least squares-discriminant analyses endorsed that farm conditions exerted an important influence on rabbit microbiota since the relative abundances of many taxa were found differentially represented between both facilities at all taxonomic levels characterized. Furthermore, only five OTUs were needed to achieve a perfect classification of samples according to the facility where animals were raised. The level of feeding and the presence of antibiotics did not modify the global alpha diversity but had an impact on some bacteria relative abundances, albeit in a small number of taxa compared with farm, which is consistent with the lower sample classification power according to these factors achieved using microbial information. Conclusions This study reveals that factors associated with the farm effect and other management factors, such as the presence of antibiotics in the diet or the feeding level, modify cecal microbial communities. It highlights the importance of offering a controlled breeding environment that reduces differences in microbial cecal composition that could be responsible for different animal performance.

scholarly journals Weak Influence of Paleoenvironmental Conditions on the Subsurface Biosphere of Lake Ohrid over the Last 515 ka

2020 ◽  
Vol 8 (11) ◽  
pp. 1736
Author(s):  
Camille Thomas ◽  
Alexander Francke ◽  
Hendrik Vogel ◽  
Bernd Wagner ◽  
Daniel Ariztegui
Keyword(s):  
Microbial Communities ◽  
Lacustrine Sediments ◽  
Environmental Parameters ◽  
Strong Relationship ◽  
Low Energy ◽  
Rrna Gene ◽  
Deep Biosphere ◽  
Lake Ohrid ◽  
Metabolic Versatility ◽  
The Impact

Lacustrine sediments are widely used to investigate the impact of climatic change on biogeochemical cycling. In these sediments, subsurface microbial communities are major actors of this cycling but can also affect the sedimentary record and overprint the original paleoenvironmental signal. We therefore investigated the subsurface microbial communities of the oldest lake in Europe, Lake Ohrid (North Macedonia, Albania), to assess the potential connection between microbial diversity and past environmental change using 16S rRNA gene sequences. Along the upper ca. 200 m of the DEEP site sediment record spanning ca. 515 thousand years (ka), our results show that Atribacteria, Bathyarchaeia and Gammaproteobacteria structured the community independently from each other. Except for the latter, these taxa are common in deep lacustrine and marine sediments due to their metabolic versatility adapted to low energy environments. Gammaproteobacteria were often co-occurring with cyanobacterial sequences or soil-related OTUs suggesting preservation of ancient DNA from the water column or catchment back to at least 340 ka, particularly in dry glacial intervals. We found significant environmental parameters influencing the overall microbial community distribution, but no strong relationship with given phylotypes and paleoclimatic signals or sediment age. Our results support a weak recording of early diagenetic processes and their actors by bulk prokaryotic sedimentary DNA in Lake Ohrid, replaced by specialized low-energy clades of the deep biosphere and a marked imprint of erosional processes on the subsurface DNA pool of Lake Ohrid.

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