scholarly journals Microbial communities of aquatic environments on Heard Island characterized by pyrotag sequencing and environmental data

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Michelle A. Allen ◽  
Ricardo Cavicchioli
Keyword(s):  
Microbial Communities ◽  
Environmental Data ◽  
Aquatic Environments ◽  
Heard Island

scholarly journals Viromes As Genetic Reservoir for the Microbial Communities in Aquatic Environments: A Focus on Antimicrobial-Resistance Genes

2017 ◽  
Vol 8 ◽  
Author(s):  
Stefano Colombo ◽  
Stefania Arioli ◽  
Eros Neri ◽  
Giulia Della Scala ◽  
Giorgio Gargari ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Microbial Communities ◽  
Resistance Genes ◽  
Aquatic Environments ◽  
Antimicrobial Resistance Genes

scholarly journals Metabarcoding under Brine: Microbial Ecology of Five Hypersaline Lakes at Rottnest Island (WA, Australia)

Water ◽  
2021 ◽  
Vol 13 (14) ◽  
pp. 1899
Author(s):  
Mattia Saccò ◽  
Nicole E. White ◽  
Matthew Campbell ◽  
Sebastian Allard ◽  
William F. Humphreys ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Aquatic Ecosystems ◽  
Taxonomic Diversity ◽  
Aquatic Environments ◽  
Community Patterns ◽  
Hypersaline Lakes ◽  
Hypersaline Ecosystems ◽  
Water Columns ◽  
Dna Metabarcoding ◽  
Influential Parameters

Hypersaline ecosystems—aquatic environments where concentration of salt exceeds 35 g L−1—host microbial communities that are highly specialised to cope with these extreme conditions. However, our knowledge on the taxonomic diversity and functional metabolisms characterising microbial communities in the water columns of hypersaline ecosystems is still limited, and this may compromise the future preservation of these unique environments. DNA metabarcoding provides a reliable and affordable tool to investigate environmental dynamics of aquatic ecosystems, and its use in brine can be highly informative. Here, we make use of bacterial 16S metabarcoding techniques combined with hydrochemical analyses to investigate the microbial patterns (diversity and functions) from five hypersaline lakes located at Rottnest Island (WA). Our results indicate lake-driven microbial aquatic assemblages that are characterised by taxonomically and functionally moderately to extremely halophilic groups, with TDS (total dissolved solids) and alkalinity amongst the most influential parameters driving the community patterns. Overall, our findings suggest that DNA metabarcoding allows rapid but reliable ecological assessment of the hypersaline aquatic microbial communities at Rottnest Island. Further studies involving different hypersaline lakes across multiple seasons will help elucidate the full extent of the potential of this tool in brine.

scholarly journals The meta-gut: Hippo inputs lead to community coalescence of animal and environmental microbiomes.

2021 ◽  
Author(s):  
Christopher Lee Dutton ◽  
Amanda L. Subalusky ◽  
Alvaro Sanchez Sanchez ◽  
Sylvie Lee Estrela ◽  
Nanxi Lu ◽  
...  
Keyword(s):  
Conceptual Framework ◽  
Microbial Communities ◽  
Gut Microbiome ◽  
Strong Influence ◽  
Ecosystem Processes ◽  
Aquatic Environments ◽  
Field Sampling ◽  
Pool Water ◽  
16S Rna

All animals carry specialized microbiomes, and their gut microbiotas in particular are continuously released into the environment through excretion of waste. Here we propose the meta-gut as a novel conceptual framework that addresses the ability of the gut microbiome released from an animal to function outside the host and potentially alter ecosystem processes mediated by microbes. An example considered here is the hippopotamus (hippo) and the pools they inhabit. Hippo pool biogeochemistry and fecal and pool water microbial communities were examined through field sampling and an experiment. Sequencing using 16S RNA methods revealed that the active microbial communities in hippo pools that received high inputs of hippo feces are more similar to the hippo gut microbiome than other nearby aquatic environments. The overlap between the microbiomes of the hippo gut and the waters into which they excrete therefore constitutes a meta-gut system with potentially strong influence on the biogeochemistry of pools and downstream waters. We propose that the meta-gut may be present where other species congregate in high densities, particularly in aquatic environments.

scholarly journals Recurrent micropollutant exposure leads to divergent degradation abilities and community succession in a freshwater microbiome

2021 ◽  
Author(s):  
Dandan Izabel-Shen ◽  
Shuang Li ◽  
Tingwei Luo ◽  
Jianjun Wang ◽  
Yan Li ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Surface Waters ◽  
Community Assembly ◽  
High Volume ◽  
Aquatic Environments ◽  
Community Succession ◽  
Microbial Dynamics ◽  
Ecological Processes ◽  
Micropollutant Removal ◽  
Deterministic Processes

The high-volume release of micropollutants into natural surface waters has raised concern due to their environmental accumulation. Persisting micropollutants can impact multiple generations of organisms via press disturbances, but their microbially-mediated degradation and the influence on community assembly remain understudied. Here, freshwater microbial communities in microcosms were treated with four common micropollutants, alone or in combination, and then transferred in stages to fresh medium containing the same level of micropollutants to mimic the recurrent exposure of microbes under environmentally relevant conditions. Our results showed that the degradation of micropollutants was closely linked to the community succession, and that recurrent exposure to micropollutants enhanced the degradation capacity. The partitioning analysis of ecological processes revealed that community assembly was dominated by stochastic processes during early exposure, via random community changes, and by deterministic processes later in the exposure. Analyzing individual taxa abundances over time revealed two distinct bacterial responses, in which a larger proportion of sensitive than tolerant taxa was present in the disturbed communities, and the abundances of the most sensitive taxa were significantly associated with micropollutant degradation. This study clearly showed that microbial communities are generally vulnerable to persisting micropollutants in aquatic environments, which has important implications for pollution management, especially regarding microbial dynamics and ecosystem functioning in micropollutant removal.

scholarly journals Evidence of Mercury Methylation and Demethylation by the Estuarine Microbial Communities Obtained in Stable Hg Isotope Studies

2018 ◽  
Vol 15 (10) ◽  
pp. 2141 ◽  
Author(s):  
Neusa Figueiredo ◽  
Maria Serralheiro ◽  
João Canário ◽  
Aida Duarte ◽  
Holger Hintelmann ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Critical Factor ◽  
High Rate ◽  
Mercury Removal ◽  
Tagus Estuary ◽  
Simultaneous Occurrence ◽  
Mercury Methylation ◽  
Aquatic Environments ◽  
Isotope Studies ◽  
Microbial Methylation

Microbial activity is a critical factor controlling methylmercury formation in aquatic environments. Microbial communities were isolated from sediments of two highly mercury-polluted areas of the Tagus Estuary (Barreiro and Cala do Norte) and differentiated according to their dependence on oxygen into three groups: aerobic, anaerobic, and sulphate-reducing microbial communities. Their potential to methylate mercury and demethylate methylmercury was evaluated through incubation with isotope-enriched Hg species (199HgCl and CH3201HgCl). The results showed that the isolated microbial communities are actively involved in methylation and demethylation processes. The production of CH3199Hg was positively correlated with sulphate-reducing microbial communities, methylating up to 0.07% of the added 199Hg within 48 h of incubation. A high rate of CH3201Hg degradation was observed and >20% of CH3201Hg was transformed. Mercury removal of inorganic forms was also observed. The results prove the simultaneous occurrence of microbial methylation and demethylation processes and indicate that microorganisms are mainly responsible for methylmercury formation and accumulation in the polluted Tagus Estuary.

The origin and fate of organic matter in circum-Arctic subglacial ecosystems

2020 ◽  
Author(s):  
Petra Vinsova ◽  
Myrna J. Simpson ◽  
Tiange Yuan ◽  
Irka Hajdas ◽  
Lukas Falteisek ◽  
...  
Keyword(s):  
Organic Matter ◽  
Microbial Community ◽  
Microbial Communities ◽  
Vascular Plant ◽  
Microbial Community Composition ◽  
Arctic Region ◽  
Environmental Data ◽  
Radiocarbon Age ◽  
Biomarker Analysis ◽  
Long Chain

<p>Glacier and ice sheet beds represent important yet underresearched cryospheric ecosystems. Life in the subglacial environment is mostly dependent on organic matter (OM) overridden by ice during times of glacier advance, and the nature of subglacial OM is, therefore, likely to drive the ecosystem functionality. Here we describe the origin, degradation stage and environmental context of OM present underneath glaciers in the circum-Arctic, and their effects on the resident microbial communities.</p><p>In total, 19 glaciers from Alaska, Greenland, Iceland, Svalbard, and Norway were sampled for subglacial sediments. Biomarker analysis of the sediment samples was conducted using total solvent extraction, and copper (II) oxide (CuO) oxidation techniques yielding lipids and lignin-derived phenols. The extracts were analyzed by GC-MS to characterize the molecular-level composition of OM present. The biomarker data were then placed in the context of other environmental data, such as radiocarbon age, nutrient contents, and microbial community composition. The majority of OM in the samples was plant-derived, suggested by the dominance of long-chain <em>n</em>-alkanols over the microbial-specific short-chain <em>n</em>-alkanols. The composition of long-chain <em>n</em>-alkanes (≥C<sub>20</sub>), used as biomarkers for vascular plant waxes, in the solvent extracts suggested grass sources for samples from most Greenland glaciers and conifer sources for some glaciers from Norway, Alaska, and Disko Island (Qeqertarsuaq) in West Greenland. The rest of the OM in the subglacial samples was identified to have more general tree sources. The carbon preference index (CPI) of long-chain <em>n</em>-alkanes suggested a high degradation stage in most samples and was correlated with the radiocarbon age of the sediments’ OC (<em>r</em> = -0.68). Sediments containing older and more degraded OM were found to host less diverse microbial communities compared to those of the younger sites.</p><p>In a rapidly warming climate, previously glacier-covered areas are being exposed as a consequence of glacier recession. This new land is standing at the onset of ecological succession and pedogenesis. Our results contribute to the understanding of the potential ecological function of subglacial OM as an important source of carbon and driver of microbial community development after deglaciation in the circum-Arctic region.</p>

scholarly journals Differences in Temperature and Water Chemistry Shape Distinct Diversity Patterns in Thermophilic Microbial Communities

2017 ◽  
Vol 83 (21) ◽  
Author(s):  
Cecilia M. Chiriac ◽  
Edina Szekeres ◽  
Knut Rudi ◽  
Andreea Baricz ◽  
Adriana Hegedus ◽  
...  
Keyword(s):  
Water Chemistry ◽  
Microbial Communities ◽  
Community Composition ◽  
Microbial Mats ◽  
Hot Spring ◽  
Environmental Data ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Thermal Gradients ◽  
Content Type

ABSTRACT This report describes the biodiversity and ecology of microbial mats developed in thermal gradients (20 to 65°C) in the surroundings of three drillings (Chiraleu [CH], Ciocaia [CI], and Mihai Bravu [MB]) tapping a hyperthermal aquifer in Romania. Using a metabarcoding approach, 16S rRNA genes were sequenced from both DNA and RNA transcripts (cDNA) and compared. The relationships between the microbial diversity and the physicochemical factors were explored. Additionally, the cDNA data were used for in silico functionality predictions, bringing new insights into the functional potential and dynamics of these communities. The results showed that each hot spring determined the formation of distinct microbial communities. In the CH mats (40 to 53°C), the abundance of Cyanobacteria decreased with temperature, opposite to those of Chloroflexi and Proteobacteria. Ectothiorhodospira, Oscillatoria, and methanogenic archaea dominated the CI communities (20 to 65°C), while the MB microbial mats (53 to 65°C) were mainly composed of Chloroflexi, Hydrogenophilus, Thermi, and Aquificae. Alpha-diversity was negatively correlated with the increase in water temperature, while beta-diversity was shaped in each hot spring by the unique combination of physicochemical parameters, regardless of the type of nucleic acid analyzed (DNA versus cDNA). The rank correlation analysis revealed a unique model that associated environmental data with community composition, consisting in the combined effect of Na+, K+, HCO3 −, and PO4 3− concentrations, together with temperature and electrical conductivity. These factors seem to determine the grouping of samples according to location, rather than with the similarities in thermal regimes, showing that other parameters beside temperature are significant drivers of biodiversity. IMPORTANCE Hot spring microbial mats represent a remarkable manifestation of life on Earth and have been intensively studied for decades. Moreover, as hot spring areas are isolated and have a limited exchange of organisms, nutrients, and energy with the surrounding environments, hot spring microbial communities can be used in model studies to elucidate the colonizing potential within extreme settings. Thus, they are of great importance in evolutionary biology, microbial ecology, and exobiology. In spite of all the efforts that have been made, the current understanding of the influence of temperature and water chemistry on the microbial community composition, diversity, and abundance in microbial mats is limited. In this study, the composition and diversity of microbial communities developed in thermal gradients in the vicinity of three hot springs from Romania were investigated, each having particular physicochemical characteristics. Our results expose new factors that could determine the formation of these ecosystems, expanding the current knowledge in this regard.

scholarly journals Metabolic overlap in environmentally diverse microbial communities

2019 ◽  
Author(s):  
Eric R. Hester ◽  
Mike S.M. Jetten ◽  
Cornelia U. Welte ◽  
Sebastian Lücker
Keyword(s):  
Microbial Communities ◽  
Future Research ◽  
Aquatic Environments ◽  
Competition And Cooperation ◽  
Microbial Species ◽  
Common Resource ◽  
Animal Hosts ◽  
Genome Scale ◽  
Genome Information ◽  
Detailed Picture

AbstractThe majority of microbial communities consist of hundreds to thousands of species, creating a massive network of organisms competing for available resources within an ecosystem. In natural microbial communities it appears that many microbial species have highly redundant metabolisms and seemingly are capable of utilizing the same substrates. This is paradoxical, as theory indicates that species requiring a common resource should outcompete one another. To better understand why microbial species can co-exist, we developed Metabolic Overlap (MO) as a new metric to survey the functional redundancy of microbial communities at the genome scale across a wide variety of ecosystems. Using metagenome-assembled genomes, we surveyed over 1200 studies across ten ecosystem types. We found the highest MO in extreme (i.e., low pH/high temperature) and aquatic environments, while the lowest MO was observed in communities associated with animal hosts, or the built/engineered environment. In addition, different metabolism subcategories were explored for their degree of metabolic overlap. For instance, overlap in nitrogen metabolism was among the lowest in Animal and Engineered ecosystems, while the most was in species from the Built environment. Together, we present a metric that utilizes whole genome information to explore overlapping niches of microbes. This provides a detailed picture of potential metabolic competition and cooperation between species present in an ecosystem, indicates the main substrate types sustaining the community and serves as a valuable tool to generate hypotheses for future research.

scholarly journals The meta-gut: community coalescence of animal gut and environmental microbiomes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Christopher L. Dutton ◽  
Amanda L. Subalusky ◽  
Alvaro Sanchez ◽  
Sylvie Estrela ◽  
Nanxi Lu ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Microbial Communities ◽  
Gut Microbiome ◽  
Animal Species ◽  
Aquatic Environments ◽  
Biogeochemical Processes ◽  
Natural Field ◽  
Field Gradients ◽  
16S Rna ◽  
Experimental Approaches

AbstractAll animals carry specialized microbiomes, and their gut microbiota are continuously released into the environment through excretion of waste. Here we propose the meta-gut as a novel conceptual framework that addresses the ability of the gut microbiome released from an animal to function outside the host and alter biogeochemical processes mediated by microbes. We demonstrate this dynamic in the hippopotamus (hippo) and the pools they inhabit. We used natural field gradients and experimental approaches to examine fecal and pool water microbial communities and aquatic biogeochemistry across a range of hippo inputs. Sequencing using 16S RNA methods revealed community coalescence between hippo gut microbiomes and the active microbial communities in hippo pools that received high inputs of hippo feces. The shared microbiome between the hippo gut and the waters into which they excrete constitutes a meta-gut system that could influence the biogeochemistry of recipient ecosystems and provide a reservoir of gut microbiomes that could influence other hosts. We propose that meta-gut dynamics may also occur where other animal species congregate in high densities, particularly in aquatic environments.

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