Primary production of freshwater microbial communities is affected by a cocktail of herbicides in an outdoor experiment

Cu pollution in coastal areas is a worldwide threat for aquatic communities. This study assesses the effects of Cu exposure on microbial diversity, community structure and functions of microbial communities in marine periphyton biofilms at environmental relevant concentrations. Periphyton was exposed for 18 days to five Cu concentrations, between 0.01 and 10 μM, in a semi-static test. Diversity and community structure of prokaryotic and eukaryotic organisms were assessed by 16S and 18S amplicon sequencing, respectively. Community function was studied as impacts on algal biomass and primary production. Additionally, we studied Pollution-Induced Community Tolerance (PICT) using photosynthesis as the endpoint. Sequencing results detected an average of 9504 and 1242 OTUs for 16S and 18S, respectively, reflecting the huge biodiversity of marine periphytic biofilms. Eukaryotes represent the most Cu-sensitive kingdom, where effects were seen already at concentrations as low as 10 nM. The structure of the prokaryotic part of the community was impacted at slightly higher concentrations (60 nM), which is still in the range of the Cu concentrations observed in the area (80 nM).The current environmental quality standard for Cu of 70 nM therefore does not seem to be sufficiently protective for periphyton. Cu exposure resulted in a more Cu-tolerant community, which was accompanied by a reduced total algal biomass, increased relative abundance of diatoms and a reduction of primary production. Cu exposure changed the network of associations between taxa in the communities. A total of 23 taxa, including species within Proteobacteria, Bacteroidetes, Stramenopiles and Hacrobia, were identified as being particularly sensitive to Cu. DNA metabarcoding is presented as a sensitive tool for community-level ecotoxicological studies that allows to observe impacts simultaneously on a multitude of pro- and eukaryotic species, and therefore to identify particularly sensitive, non-cultivable species and taxa.

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Microbial communities and geochemical dynamics in an extremely acidic, metal-rich stream at an abandoned sulfide mine (Huelva, Spain) underpinned by two functional primary production systems

Environmental Microbiology ◽

10.1111/j.1462-2920.2007.01294.x ◽

2007 ◽

Vol 9 (7) ◽

pp. 1761-1771 ◽

Cited By ~ 131

Author(s):

Owen F. Rowe ◽

Javier Sánchez-España ◽

Kevin B. Hallberg ◽

D. Barrie Johnson

Keyword(s):

Primary Production ◽

Microbial Communities ◽

Production Systems

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Sea ice microbial communities. VI. Growth and primary production in bottom ice under graded snow cover

Marine Ecology Progress Series ◽

10.3354/meps035153 ◽

1987 ◽

Vol 35 ◽

pp. 153-164 ◽

Cited By ~ 91

Author(s):

SM Grossi ◽

ST Kottmeier ◽

RL Moe ◽

GT Taylor ◽

CW Sullivan

Keyword(s):

Sea Ice ◽

Primary Production ◽

Microbial Communities ◽

Snow Cover

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Microdiversity characterizes prevalent phylogenetic clades in the glacier-fed stream microbiome

The ISME Journal ◽

10.1038/s41396-021-01106-6 ◽

2021 ◽

Author(s):

Stilianos Fodelianakis ◽

Alex D. Washburne ◽

Massimo Bourquin ◽

Paraskevi Pramateftaki ◽

Tyler J. Kohler ◽

...

Keyword(s):

New Zealand ◽

Primary Production ◽

Microbial Communities ◽

Analytical Framework ◽

Α Diversity ◽

High Prevalence ◽

Ecological Success ◽

Underlying Mechanisms

AbstractGlacier-fed streams (GFSs) are extreme and rapidly vanishing ecosystems, and yet they harbor diverse microbial communities. Although our understanding of the GFS microbiome has recently increased, we do not know which microbial clades are ecologically successful in these ecosystems, nor do we understand potentially underlying mechanisms. Ecologically successful clades should be more prevalent across GFSs compared to other clades, which should be reflected as clade-wise distinctly low phylogenetic turnover. However, methods to assess such patterns are currently missing. Here we developed and applied a novel analytical framework, “phyloscore analysis”, to identify clades with lower spatial phylogenetic turnover than other clades in the sediment microbiome across twenty GFSs in New Zealand. These clades constituted up to 44% and 64% of community α-diversity and abundance, respectively. Furthermore, both their α-diversity and abundance increased as sediment chlorophyll a decreased, corroborating their ecological success in GFS habitats largely devoid of primary production. These clades also contained elevated levels of putative microdiversity than others, which could potentially explain their high prevalence in GFSs. This hitherto unknown microdiversity may be threatened as glaciers shrink, urging towards further genomic and functional exploration of the GFS microbiome.

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Chemolithotrophic Primary Production in a Subglacial Ecosystem

Applied and Environmental Microbiology ◽

10.1128/aem.01956-14 ◽

2014 ◽

Vol 80 (19) ◽

pp. 6146-6153 ◽

Cited By ~ 57

Author(s):

Eric S. Boyd ◽

Trinity L. Hamilton ◽

Jeff R. Havig ◽

Mark L. Skidmore ◽

Everett L. Shock

Keyword(s):

Primary Production ◽

Microbial Communities ◽

Primary Productivity ◽

Iron Sulfide ◽

Pyrite Oxidation ◽

Mineral Dissolution ◽

Bisphosphate Carboxylase ◽

Content Type ◽

Sulfate Production ◽

Subglacial Environment

ABSTRACTGlacial comminution of bedrock generates fresh mineral surfaces capable of sustaining chemotrophic microbial communities under the dark conditions that pervade subglacial habitats. Geochemical and isotopic evidence suggests that pyrite oxidation is a dominant weathering process generating protons that drive mineral dissolution in many subglacial systems. Here, we provide evidence correlating pyrite oxidation with chemosynthetic primary productivity and carbonate dissolution in subglacial sediments sampled from Robertson Glacier (RG), Alberta, Canada. Quantification and sequencing of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) transcripts suggest that populations closely affiliated withSideroxydans lithotrophicus, an iron sulfide-oxidizing autotrophic bacterium, are abundant constituents of microbial communities at RG. Microcosm experiments indicate sulfate production during biological assimilation of radiolabeled bicarbonate. Geochemical analyses of subglacial meltwater indicate that increases in sulfate levels are associated with increased calcite and dolomite dissolution. Collectively, these data suggest a role for biological pyrite oxidation in driving primary productivity and mineral dissolution in a subglacial environment and provide the first rate estimate for bicarbonate assimilation in these ecosystems. Evidence for lithotrophic primary production in this contemporary subglacial environment provides a plausible mechanism to explain how subglacial communities could be sustained in near-isolation from the atmosphere during glacial-interglacial cycles.

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Copper affects composition and functions of microbial communities in marine biofilms at environmentally relevant concentrations

10.7287/peerj.preprints.27129v1 ◽

2018 ◽

Author(s):

Natàlia Corcoll ◽

Jianghua Yang ◽

Thomas Backhaus ◽

Xiaowei Zhang ◽

Martin Karl Eriksson ◽

...

Keyword(s):

Community Structure ◽

Primary Production ◽

Microbial Communities ◽

Algal Biomass ◽

Amplicon Sequencing ◽

Quality Standard ◽

Aquatic Communities ◽

Static Test ◽

Community Function ◽

Eukaryotic Organisms

Cu pollution in coastal areas is a worldwide threat for aquatic communities. This study assesses the effects of Cu exposure on microbial diversity, community structure and functions of microbial communities in marine periphyton biofilms at environmental relevant concentrations. Periphyton was exposed for 18 days to five Cu concentrations, between 0.01 and 10 μM, in a semi-static test. Diversity and community structure of prokaryotic and eukaryotic organisms were assessed by 16S and 18S amplicon sequencing, respectively. Community function was studied as impacts on algal biomass and primary production. Additionally, we studied Pollution-Induced Community Tolerance (PICT) using photosynthesis as the endpoint. Sequencing results detected an average of 9504 and 1242 OTUs for 16S and 18S, respectively, reflecting the huge biodiversity of marine periphytic biofilms. Eukaryotes represent the most Cu-sensitive kingdom, where effects were seen already at concentrations as low as 10 nM. The structure of the prokaryotic part of the community was impacted at slightly higher concentrations (60 nM), which is still in the range of the Cu concentrations observed in the area (80 nM).The current environmental quality standard for Cu of 70 nM therefore does not seem to be sufficiently protective for periphyton. Cu exposure resulted in a more Cu-tolerant community, which was accompanied by a reduced total algal biomass, increased relative abundance of diatoms and a reduction of primary production. Cu exposure changed the network of associations between taxa in the communities. A total of 23 taxa, including species within Proteobacteria, Bacteroidetes, Stramenopiles and Hacrobia, were identified as being particularly sensitive to Cu. DNA metabarcoding is presented as a sensitive tool for community-level ecotoxicological studies that allows to observe impacts simultaneously on a multitude of pro- and eukaryotic species, and therefore to identify particularly sensitive, non-cultivable species and taxa.

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Thiamine metabolism genes in diatoms are not regulated by thiamine despite the presence of predicted riboswitches

10.1101/2022.01.04.474978 ◽

2022 ◽

Author(s):

Marcel Llavero-Pasquina ◽

Katrin Geisler ◽

Andre Holzer ◽

Payam Mehrshahi ◽

Gonzalo I Mendoza-Ochoa ◽

...

Keyword(s):

Primary Production ◽

Microbial Communities ◽

Phaeodactylum Tricornutum ◽

Gene Editing ◽

Targeted Mutagenesis ◽

Thiamine Pyrophosphate ◽

Thiamine Metabolism ◽

Targeted Mutation ◽

Marine Microbial Communities ◽

Thiamine Biosynthesis

Thiamine pyrophosphate (TPP), an essential co-factor for all species, is biosynthesised through a metabolically expensive pathway regulated by TPP riboswitches in bacteria, fungi, plants and green algae. Diatoms are microalgae responsible for approximately 20% of global primary production. They have been predicted to contain TPP aptamers in the 3'UTR of some thiamine metabolism-related genes, but little is known about their function and regulation. We used bioinformatics, antimetabolite growth assays, RT-qPCR, targeted mutagenesis and reporter constructs to test whether the predicted TPP riboswitches respond to thiamine supplementation in diatoms. Gene editing was used to investigate the functions of the genes with associated TPP riboswitches in Phaeodactylum tricornutum. We found that thiamine-related genes with putative TPP aptamers are not responsive to thiamine or its precursor 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP), and the targeted mutation of the TPP aptamer in the HMP-P synthase (THIC) does not deregulate thiamine biosynthesis in P. tricornutum. Through genome editing we established that PtSSSP is necessary for thiamine uptake and that PtTHIC is essential for thiamine biosynthesis. Our results highlight the importance of experimentally testing bioinformatic aptamer predictions and provide new insights into the thiamine metabolism shaping the structure of marine microbial communities with global biogeochemical importance.

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A peek in the micro-sized world: a review of design principles, engineering tools, and applications of engineered microbial community

Biochemical Society Transactions ◽

10.1042/bst20190172 ◽

2020 ◽

Vol 48 (2) ◽

pp. 399-409

Author(s):

Baizhen Gao ◽

Rushant Sabnis ◽

Tommaso Costantini ◽

Robert Jinkerson ◽

Qing Sun

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Environmental Remediation ◽

Real Life ◽

Design Principles ◽

Microbial Interactions ◽

Potential Applications ◽

New Gene ◽

Global Biogeochemical Cycles ◽

Synthetic Microbial Communities

Microbial communities drive diverse processes that impact nearly everything on this planet, from global biogeochemical cycles to human health. Harnessing the power of these microorganisms could provide solutions to many of the challenges that face society. However, naturally occurring microbial communities are not optimized for anthropogenic use. An emerging area of research is focusing on engineering synthetic microbial communities to carry out predefined functions. Microbial community engineers are applying design principles like top-down and bottom-up approaches to create synthetic microbial communities having a myriad of real-life applications in health care, disease prevention, and environmental remediation. Multiple genetic engineering tools and delivery approaches can be used to ‘knock-in' new gene functions into microbial communities. A systematic study of the microbial interactions, community assembling principles, and engineering tools are necessary for us to understand the microbial community and to better utilize them. Continued analysis and effort are required to further the current and potential applications of synthetic microbial communities.

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