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.

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.

scholarly journals Microbial Signatures in Deep CO2-Saturated Miocene Sediments of the Active Hartoušov Mofette System (NW Czech Republic)

2020 ◽  
Vol 11 ◽  
Author(s):  
Qi Liu ◽  
Karsten Adler ◽  
Daniel Lipus ◽  
Horst Kämpf ◽  
Robert Bussert ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Dna Analysis ◽  
Quantitative Polymerase Chain Reaction ◽  
Lacustrine Sediments ◽  
Deep Biosphere ◽  
Upward Migration ◽  
Eger Rift ◽  
And Migration ◽  
Cheb Basin ◽  
The Impact

The Hartoušov mofette system is a natural CO2 degassing site in the central Cheb Basin (Eger Rift, Central Europe). In early 2016 a 108 m deep core was obtained from this system to investigate the impact of ascending mantle-derived CO2 on indigenous deep microbial communities and their surrounding life habitat. During drilling, a CO2 blow out occurred at a depth of 78.5 meter below surface (mbs) suggesting a CO2 reservoir associated with a deep low-permeable CO2-saturated saline aquifer at the transition from Early Miocene terrestrial to lacustrine sediments. Past microbial communities were investigated by hopanoids and glycerol dialkyl glycerol tetraethers (GDGTs) reflecting the environmental conditions during the time of deposition rather than showing a signal of the current deep biosphere. The composition and distribution of the deep microbial community potentially stimulated by the upward migration of CO2 starting during Mid Pleistocene time was investigated by intact polar lipids (IPLs), quantitative polymerase chain reaction (qPCR), and deoxyribonucleic acid (DNA) analysis. The deep biosphere is characterized by microorganisms that are linked to the distribution and migration of the ascending CO2-saturated groundwater and the availability of organic matter instead of being linked to single lithological units of the investigated rock profile. Our findings revealed high relative abundances of common soil and water bacteria, in particular the facultative, anaerobic and potential iron-oxidizing Acidovorax and other members of the family Comamonadaceae across the whole recovered core. The results also highlighted the frequent detection of the putative sulfate-oxidizing and CO2-fixating genus Sulfuricurvum at certain depths. A set of new IPLs are suggested to be indicative for microorganisms associated to CO2 accumulation in the mofette system.

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.

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 Salinity-triggered compositional and metabolic responses of autotrophic prokaryotes in Tibetan lacustrine sediments

2020 ◽  
Author(s):  
Jun Liu ◽  
Yun Fang ◽  
Jian Yang ◽  
Hongchen Jiang ◽  
Brian P. Hedlund ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Aquatic Ecosystems ◽  
Carbon Fixation ◽  
Net Primary Production ◽  
Salinity Gradient ◽  
Lacustrine Sediments ◽  
Ecological Niches ◽  
Dissimilatory Sulfate Reduction ◽  
Physiological Efficiency ◽  
Metabolic Versatility

Abstract Background Autotrophic prokaryotes are crucial participants in the global carbon cycle, and autotrophic carbon fixation contributes approximately 50% of the global net primary production in aquatic ecosystems per year. Salinity is a prominent regulator structuring microbial communities in diverse aquatic ecosystems. However, little information is available regarding the compositional and physiological response of autotrophic microbial communities to salinity change. Here, we used genome-resolved metagenomics to study autotrophic microbial communities in 25 Tibetan lacustrine sediments with a salinity gradient (from 0.54‰ to 82.6‰). Results117 metagenome-assembled genomes (MAGs) with carbon fixation potential belonging to 12 phyla were retrieved, of which approximately 21% were not affiliated with the known orders, suggesting taxonomically diverse autotrophic assemblages in sediments. The total abundance of these putative autotrophs decreased significantly with increasing salinity, and the variation of sediment autotrophic communities was mainly driven by salinity, pH and TOC. Notably, a change in the predominant lineage from Betaproteobacteria to Deltaproteobacteria was observed along the salinity gradient, and the dominant pathway for carbon fixation shifted from the Calvin-Benson-Bassham (CBB) cycle to more energy efficient Wood-Lungdahl (WL) pathway with glycolysis from Entner-Doudoroff to more exergonic Embden-Meyerhof-Parnas, demonstrating that the physiological efficiency increases from freshwater to hypersaline autotrophic communities. Metabolic inference revealed major links for carbon fixation to the oxidation of reduced sulfur compounds, ferrous iron and carbon monoxide, denitrification and nitrogen fixation in these MAGs, as well as the occurrence of dissimilatory sulfate reduction and the WL pathway dominating hypersaline sediments, greatly extending the understanding of metabolic versatility and diverse ecological niches of autotrophic microorganisms. Conclusions This study provided a systematic attempt to characterize the response of carbon fixation pathways to salinity and the knowledge essential for revealing ecological roles of autotrophic prokaryotes in aquatic habitats. These findings suggest with increased salinity, physiological efficiency of the autotrophic community increases, which has important implications for understanding the carbon budget in aquatic ecosystems.

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.

scholarly journals Spatial and temporal constraints on the composition of microbial communities in subsurface boreholes of the Edgar Experimental Mine

2021 ◽  
Author(s):  
Patrick H. Thieringer ◽  
Alexander S. Honeyman ◽  
John R. Spear
Keyword(s):  
Microbial Communities ◽  
Spatial Scales ◽  
Microbial Community Composition ◽  
Rrna Gene ◽  
Deep Biosphere ◽  
Surface Hydrology ◽  
Microbial Composition ◽  
16S Rrna Gene Analysis ◽  
High Concentrations ◽  
Recharge Rates

The deep biosphere hosts uniquely adapted microorganisms overcoming geochemical extremes at significant depths within the crust of the Earth. While numerous novel microbial members with unique physiological modifications remain to be identified, even greater attention is required to understand the near-subsurface and its continuity with surface systems. This raises key questions about networking of surface hydrology, geochemistry affecting near-subsurface microbial composition, and resiliency of subsurface ecosystems. Here, we apply molecular biological and geochemical approaches to determine temporal microbial composition and environmental conditions of filtered borehole fluid from the Edgar Experimental Mine (~150 meters below the surface) in Idaho Springs, CO. Samples were collected over a 4-year collection period from expandable packers deployed to accumulate fluid in previously drilled boreholes located centimeters to meters apart, revealing temporal evolution of borehole microbiology. Meteoric water feeding boreholes demonstrated variable recharge rates due to a complex and undefined fracture system within the host rock. 16S rRNA gene analysis determined unique microbial communities occupy the four boreholes examined. Two boreholes yielded sequences revealing the presence of Proteobacteria, Firmicutes, and Nanoarcheota associated with endemic subsurface communities. Two other boreholes presented sequences related to soil-originating microbiota, which likely indicate a direct link to surface infiltration. High concentrations of sulfate suggest sulfur-related metabolic strategies dominate within these near-subsurface boreholes. Overall, results indicate microbial community composition in the near-subsurface is highly dynamic at very fine spatial scales (<20cm) within fluid-rock equilibrated boreholes, which additionally supports the role of a relationship for surface geochemical processes infiltrating and influencing subsurface environments.

scholarly journals Urbanization promotes specific bacteria in freshwater microbiomes including potential pathogens

2020 ◽  
Author(s):  
Daniela Numberger ◽  
Luca Zoccarato ◽  
Jason Woodhouse ◽  
Lars Ganzert ◽  
Sascha Sauer ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Treatment Plant ◽  
Environmental Parameters ◽  
Local Environment ◽  
Freshwater Ecosystems ◽  
Urban Environments ◽  
Rrna Gene ◽  
Global Increase ◽  
Bacterial Groups

ABSTRACTFreshwater ecosystems are not closed or sterile environments. They support complex and highly dynamic microbiological communities strongly structured by their local environment. Growing city populations and the process of urbanization is predicted to strongly alter freshwater environments. To determine the changes in freshwater microbial communities associated with urbanization, full-length 16S rRNA gene PacBio sequencing was performed on DNA from surface water and sediments from five lakes and a wastewater treatment plant in the Berlin-Brandenburg region of Germany. Water samples exhibited highly environment specific bacterial communities with multiple genera showing clear urban signatures. We identified potential harmful bacterial groups that were strongly associated with environmental parameters specific to urban environments such as Clostridium, Neisseria, Streptococcus, Yersinia and the toxic cyanobacterial genus Microcystis. We demonstrate that urbanization can alter natural microbial communities in lakes and promote specific bacterial genera which include potential pathogens. Urbanization, creates favourable conditions for pathogens that might be introduced by sporadic events or shift their proportions within the ecosystem. Our findings are of global relevance representing a long-term health risk in urbanized waterbodies at a time of global increase in urbanization.

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;

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