Environmental influences shaping microbial communities in low oxygen, highly stratified marine embayment

AbstractMicrobial communities in oxygen minimum zones (OMZs) are known to have significant impacts on global biogeochemical cycles, but viral influence on microbial processes in these regions are much less studied. Here we provide baseline ecological patterns using microscopy and viral metagenomics from the Eastern Tropical North Pacific (ETNP) OMZ region that enhance our understanding of viruses in these climate-critical systems. While extracellular viral abundance decreased below the oxycline, viral diversity and lytic infection frequency remained high within the OMZ, demonstrating that viral influences on microbial communities were still substantial without the detectable presence of oxygen. Viral community composition was strongly related to oxygen concentration, with viral populations in low-oxygen portions of the water column being distinct from their surface layer counterparts. However, this divergence was not accompanied by the expected differences in viral-encoded auxiliary metabolic genes (AMGs) relating to nitrogen and sulfur metabolisms that are known to be performed by microbial communities in these low-oxygen and anoxic regions. Instead, several abundant AMGs were identified in the oxycline and OMZ that may modulate host responses to low-oxygen stress. We hypothesize that this is due to selection for viral-encoded genes that influence host survivability rather than modulating host metabolic reactions within the ETNP OMZ. Together, this study shows that viruses are not only diverse throughout the water column in the ETNP, including the OMZ, but their infection of microorganisms has the potential to alter host physiological state within these biogeochemically important regions of the ocean.

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Aura-biomes are present in the water layer above coral reef benthic macro-organisms

PeerJ ◽

10.7717/peerj.3666 ◽

2017 ◽

Vol 5 ◽

pp. e3666 ◽

Cited By ~ 8

Author(s):

Kevin Walsh ◽

J. Matthew Haggerty ◽

Michael P. Doane ◽

John J. Hansen ◽

Megan M. Morris ◽

...

Keyword(s):

Coral Reef ◽

Microbial Communities ◽

Water Column ◽

Coral Cover ◽

Coral Disease ◽

Benthic Organism ◽

Low Oxygen ◽

Surrounding Water ◽

Stressful Environment ◽

Turf Algae

As coral reef habitats decline worldwide, some reefs are transitioning from coral- to algal-dominated benthos with the exact cause for this shift remaining elusive. Increases in the abundance of microbes in the water column has been correlated with an increase in coral disease and reduction in coral cover. Here we investigated how multiple reef organisms influence microbial communities in the surrounding water column. Our study consisted of a field assessment of microbial communities above replicate patches dominated by a single macro-organism. Metagenomes were constructed from 20 L of water above distinct macro-organisms, including (1) the coral Mussismilia braziliensis, (2) fleshy macroalgae (Stypopodium, Dictota and Canistrocarpus), (3) turf algae, and (4) the zoanthid Palythoa caribaeorum and were compared to the water microbes collected 3 m above the reef. Microbial genera and functional potential were annotated using MG-RAST and showed that the dominant benthic macro-organisms influence the taxa and functions of microbes in the water column surrounding them, developing a specific “aura-biome”. The coral aura-biome reflected the open water column, and was associated with Synechococcus and functions suggesting oligotrophic growth, while the fleshy macroalgae aura-biome was associated with Ruegeria, Pseudomonas, and microbial functions suggesting low oxygen conditions. The turf algae aura-biome was associated with Vibrio, Flavobacterium, and functions suggesting pathogenic activity, while zoanthids were associated with Alteromonas and functions suggesting a stressful environment. Because each benthic organism has a distinct aura-biome, a change in benthic cover will change the microbial community of the water, which may lead to either the stimulation or suppression of the recruitment of benthic organisms.

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Relationships between pond water and tilapia skin microbiomes in aquaculture ponds in Malawi

10.1101/2021.12.06.470702 ◽

2021 ◽

Author(s):

Jamie McMurtrie ◽

Shayma Alathari ◽

Dominique L. Chaput ◽

David Bass ◽

Camerson Ghambi ◽

...

Keyword(s):

Microbial Communities ◽

Water Samples ◽

Environmental Influences ◽

Disease Onset ◽

Fish Farming ◽

Pond Water ◽

List Type ◽

Fish Skin ◽

Surrounding Water ◽

Aquaculture Ponds

AbstractIntensification of fish farming practices is being driven by the demand for increased food production to support a rapidly growing global human population, particularly in lower-middle income countries. Intensification of production, however, increases the risk of disease outbreaks and thus likelihood for crop losses. The microbial communities that colonise the skin mucosal surface of fish are poorly understood, but are important in maintaining fish health and resistance against disease. This skin microbial community is susceptible to disruption through stressors associated with transport, handling and the environment of intensive practices, and this risks the propagation of disease-causing pathogens. In this study, we characterised the microbial assemblages found on tilapia skin — the most widely farmed finfish globally — and in the surrounding water of seven earthen aquaculture ponds from two pond systems in distinct geographic regions in Malawi. Metabarcoding approaches were used to sequence the prokaryotic and microeukaryotic communities. We found 92% of prokaryotic amplicon sequence variants were common to both skin and water samples. Differentially enriched and core taxa, however, differed between the skin and water samples. In tilapia skin, Cetobacterium, Paucibacter, Pseudomonas and Comamonadaceae were enriched, whereas, the cyanobacteria Cyanobium, Microcystis and/or Synechocystis, and the diatom Cyclotella, were most prevalent in pond water. Ponds that clustered together according to their water prokaryotic communities also had similar microeukaryotic communities indicating strong environmental influences on prokaryotic and microeukaryotic community structures. While strong site-specific clustering was observed in pond water, the grouping of tilapia skin prokaryotes by pond site was less distinct, suggesting fish microbiota have a greater buffering capacity against environmental influences. The characterised diversity, structure and variance of microbial communities associated with tilapia culture in Malawi provides the baseline for studies on how future intensification practices may lead to microbial dysbiosis and disease onset.HighlightsTilapia skin communities vary in different ponds but share some common taxaPond sites have a stronger influence on water microbiome community structure than in fish skinSelected skin-associated taxa could be used to monitor dysbiotic eventsThe fish skin microeukaryotic community is complex and poorly characterised

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The Diversity and Evolution of Microbial Dissimilatory Phosphite Oxidation

10.1101/2020.12.28.424620 ◽

2020 ◽

Author(s):

Sophia D. Ewens ◽

Alexa F. S. Gomberg ◽

Tyler P. Barnum ◽

Mikayla A. Borton ◽

Hans K. Carlson ◽

...

Keyword(s):

Microbial Communities ◽

Phylogenetic Analyses ◽

Taxonomic Diversity ◽

Metagenomic Sequencing ◽

Low Oxygen ◽

Cell Potential ◽

Environmental Distribution ◽

Metabolic Versatility ◽

Anoxic Environments ◽

Geochemical Models

AbstractPhosphite is the most energetically favorable chemotrophic electron donor known, with a half-cell potential (E°’) of −650 mV for the PO43-/PO33- couple. Since the discovery of microbial dissimilatory phosphite oxidation (DPO) in 2000, the environmental distribution, evolution, and diversity of DPO microorganisms (DPOM) has remained enigmatic and only two species have been identified. Here metagenomic sequencing of phosphite enriched microbial communities enabled the reconstruction and metabolic characterization of 21 novel DPOM. These DPOM spanned six classes of bacteria, including the Negativicutes, Desulfotomaculia, Synergistia, Syntrophia, Desulfobacteria and Desulfomonilia_A. Comparing the DPO genes from the genomes of enriched organisms to over 17,000 publicly available metagenomes revealed the global existence of this metabolism in diverse anoxic environments, including wastewaters, sediments, and subsurface aquifers. Despite their newfound environmental and taxonomic diversity, metagenomic analyses suggested that the typical DPOM is a chemolithoautotroph that occupies low-oxygen environments and specializes in phosphite oxidation coupled to CO2 reduction. Phylogenetic analyses indicated that the DPO genes form a highly conserved cluster that likely has ancient origins predating the split of monoderm and diderm bacteria. By coupling microbial cultivation strategies with metagenomics, these studies highlighted the unsampled metabolic versatility latent in microbial communities. We have uncovered the unexpected prevalence, diversity, biochemical specialization, and ancient origins of a unique metabolism central to the redox cycling of phosphorus, a primary nutrient on earth.Significance StatementGeochemical models of the phosphorus (P) cycle uniquely ignore microbial redox transformations. Yet phosphite is a reduced P source that has been detected in several environments at concentrations that suggest a contemporary P redox cycle. Microbial dissimilatory phosphite oxidation (DPO) converts soluble phosphite into phosphate, and a false notion of rarity has limited our understanding of its diversity and environmental distribution. Here we demonstrate that DPO is an ancient energy metabolism hosted by taxonomically diverse, autotrophic bacteria that exist globally throughout anoxic environments. DPO microorganisms are therefore likely to have provided bioavailable phosphate and fixed carbon to anoxic ecosystems throughout Earth’s history and continue to do so in contemporary environments.

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The diversity and evolution of microbial dissimilatory phosphite oxidation

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2020024118 ◽

2021 ◽

Vol 118 (11) ◽

pp. e2020024118

Author(s):

Sophia D. Ewens ◽

Alexa F. S. Gomberg ◽

Tyler P. Barnum ◽

Mikayla A. Borton ◽

Hans K. Carlson ◽

...

Keyword(s):

Microbial Communities ◽

Phylogenetic Analyses ◽

Taxonomic Diversity ◽

Metagenomic Sequencing ◽

Low Oxygen ◽

Cell Potential ◽

Environmental Distribution ◽

Metabolic Versatility ◽

Anoxic Environments

Phosphite is the most energetically favorable chemotrophic electron donor known, with a half-cell potential (Eo′) of −650 mV for the PO43−/PO33− couple. Since the discovery of microbial dissimilatory phosphite oxidation (DPO) in 2000, the environmental distribution, evolution, and diversity of DPO microorganisms (DPOMs) have remained enigmatic, as only two species have been identified. Here, metagenomic sequencing of phosphite-enriched microbial communities enabled the genome reconstruction and metabolic characterization of 21 additional DPOMs. These DPOMs spanned six classes of bacteria, including the Negativicutes, Desulfotomaculia, Synergistia, Syntrophia, Desulfobacteria, and Desulfomonilia_A. Comparing the DPO genes from the genomes of enriched organisms with over 17,000 publicly available metagenomes revealed the global existence of this metabolism in diverse anoxic environments, including wastewaters, sediments, and subsurface aquifers. Despite their newfound environmental and taxonomic diversity, metagenomic analyses suggested that the typical DPOM is a chemolithoautotroph that occupies low-oxygen environments and specializes in phosphite oxidation coupled to CO2 reduction. Phylogenetic analyses indicated that the DPO genes form a highly conserved cluster that likely has ancient origins predating the split of monoderm and diderm bacteria. By coupling microbial cultivation strategies with metagenomics, these studies highlighted the unsampled metabolic versatility latent in microbial communities. We have uncovered the unexpected prevalence, diversity, biochemical specialization, and ancient origins of a unique metabolism central to the redox cycling of phosphorus, a primary nutrient on Earth.

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The effect of exposure to high altitude and low oxygen on intestinal microbial communities in mice

PLoS ONE ◽

10.1371/journal.pone.0203701 ◽

2018 ◽

Vol 13 (9) ◽

pp. e0203701 ◽

Cited By ~ 6

Author(s):

Wei Zhang ◽

Lefei Jiao ◽

Ruixin Liu ◽

Yu Zhang ◽

Qiaorong Ji ◽

...

Keyword(s):

High Altitude ◽

Microbial Communities ◽

Low Oxygen

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Gulf of Mexico blue hole harbors high levels of novel microbial lineages

10.1101/2020.10.18.342550 ◽

2020 ◽

Author(s):

NV Patin ◽

ZA Dietrich ◽

A Stancil ◽

M Quinan ◽

JS Beckler ◽

...

Keyword(s):

Gulf Of Mexico ◽

Microbial Communities ◽

Organic Matter Content ◽

Bottom Layer ◽

Microbial Evolution ◽

Matter Content ◽

Low Oxygen ◽

Blue Hole ◽

Hypoxic Zone ◽

Geochemical Profiles

AbstractExploration of oxygen-depleted marine environments has consistently revealed novel microbial taxa and metabolic capabilities that expand our understanding of microbial evolution and ecology. Marine blue holes are shallow karst formations characterized by low oxygen and high organic matter content. They are logistically challenging to sample, and thus our understanding of their biogeochemistry and microbial ecology is limited. We present a metagenomic characterization of Amberjack Hole on the Florida continental shelf (Gulf of Mexico). Dissolved oxygen became depleted at the hole’s rim (32 m water depth), remained low but detectable in an intermediate hypoxic zone (40-75 m), and then increased to a secondary peak before falling below detection in the bottom layer (80-110 m), concomitant with increases in nutrients, dissolved iron, and a series of sequentially more reduced sulfur species. Microbial communities in the bottom layer contained heretofore undocumented levels of the recently discovered phylum Woesearchaeota (up to 58% of the community), along with lineages in the bacterial Candidate Phyla Radiation (CPR). Thirty-one high-quality metagenome-assembled genomes (MAGs) showed extensive biochemical capabilities for sulfur and nitrogen cycling, as well as for resisting and respiring arsenic. One uncharacterized gene associated with a CPR lineage differentiated hypoxic from anoxic zone communities. Overall, microbial communities and geochemical profiles were stable across two sampling dates in the spring and fall of 2019. The blue hole habitat is a natural marine laboratory that provides opportunities for sampling taxa with under-characterized but potentially important roles in redox-stratified microbial processes.

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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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HIF1-α-Mediated Gene Expression Induced by Vitamin B1 Deficiency

International Journal for Vitamin and Nutrition Research ◽

10.1024/0300-9831/a000159 ◽

2013 ◽

Vol 83 (3) ◽

pp. 188-197 ◽

Cited By ~ 21

Author(s):

Rebecca L. Sweet ◽

Jason A. Zastre

Keyword(s):

Gene Expression ◽

Thiamine Deficiency ◽

Glucose Transporter ◽

Neuroblastoma Cell ◽

Hypoxia Inducible Factor ◽

Clinical Manifestations ◽

Vitamin B1 ◽

Low Oxygen ◽

Glucose Transporter 1 ◽

Metabolic Intermediates

It is well established that thiamine deficiency results in an excess of metabolic intermediates such as lactate and pyruvate, which is likely due to insufficient levels of cofactor for the function of thiamine-dependent enzymes. When in excess, both pyruvate and lactate can increase the stabilization of the hypoxia-inducible factor 1-alpha (HIF-1α) transcription factor, resulting in the trans-activation of HIF-1α regulated genes independent of low oxygen, termed pseudo-hypoxia. Therefore, the resulting dysfunction in cellular metabolism and accumulation of pyruvate and lactate during thiamine deficiency may facilitate a pseudo-hypoxic state. In order to investigate the possibility of a transcriptional relationship between hypoxia and thiamine deficiency, we measured alterations in metabolic intermediates, HIF-1α stabilization, and gene expression. We found an increase in intracellular pyruvate and extracellular lactate levels after thiamine deficiency exposure to the neuroblastoma cell line SK-N-BE. Similar to cells exposed to hypoxia, there was a corresponding increase in HIF-1α stabilization and activation of target gene expression during thiamine deficiency, including glucose transporter-1 (GLUT1), vascular endothelial growth factor (VEGF), and aldolase A. Both hypoxia and thiamine deficiency exposure resulted in an increase in the expression of the thiamine transporter SLC19A3. These results indicate thiamine deficiency induces HIF-1α-mediated gene expression similar to that observed in hypoxic stress, and may provide evidence for a central transcriptional response associated with the clinical manifestations of thiamine deficiency.

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Behavioral Testing of Mice Concerning Anxiety and Depression

Zeitschrift für Psychologie ◽

10.1027/2151-2604/a000215 ◽

2015 ◽

Vol 223 (3) ◽

pp. 151-156 ◽

Cited By ~ 1

Author(s):

Nina Schweinfurth ◽

Undine E. Lang

Keyword(s):

Environmental Influences ◽

Sickness Behavior ◽

Laboratory Research ◽

Anxiety And Depression ◽

Housing Conditions ◽

Human Beings ◽

Behavioral Testing ◽

New Developments ◽

Animal Trials ◽

Resilience Factors

Abstract. In the development of new psychiatric drugs and the exploration of their efficacy, behavioral testing in mice has always shown to be an inevitable procedure. By studying the behavior of mice, diverse pathophysiological processes leading to depression, anxiety, and sickness behavior have been revealed. Moreover, laboratory research in animals increased at least the knowledge about the involvement of a multitude of genes in anxiety and depression. However, multiple new possibilities to study human behavior have been developed recently and improved and enable a direct acquisition of human epigenetic, imaging, and neurotransmission data on psychiatric pathologies. In human beings, the high influence of environmental and resilience factors gained scientific importance during the last years as the search for key genes in the development of affective and anxiety disorders has not been successful. However, environmental influences in human beings themselves might be better understood and controllable than in mice, where environmental influences might be as complex and subtle. The increasing possibilities in clinical research and the knowledge about the complexity of environmental influences and interferences in animal trials, which had been underestimated yet, question more and more to what extent findings from laboratory animal research translate to human conditions. However, new developments in behavioral testing of mice involve the animals’ welfare and show that housing conditions of laboratory mice can be markedly improved without affecting the standardization of results.

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