Genome and community-level interaction insights on wide carbon utilizing and element cycling function of Hydrothermarchaeota from hydrothermal sediment

AbstractHydrothermal vents release reduced compounds and small organic carbons into surrounding seawaters, providing essential substrates for microbial-derived biosynthesis and bioenergy transformations. Despite the wide distribution of Marine Benthic Group-E archaea (referred to as Hydrothermarchaeota) in hydrothermal environments, little is known on their genome blueprints and ecofunctions. Here, we studied four relatively high-completeness (> 80%) metagenome-assembled genomes (MAGs) from a black smoker chimney and surrounding sulfide sediments in the Mid-Atlantic Ridge of the South Atlantic Ocean (BSmoChi-MAR) as well as publicly available datasets. Comparative genomics suggest that Hydrothermarchaeota members have versatile carbon metabolism, including assimilating proteins, lactate and acetate, degrading aromatics anaerobically, oxidizing C1 compounds (CO, formate, and formaldehyde), utilizing methyl-compounds, and incorporating CO2 by tetrahydromethanopterin-based Wood–Ljungdahl (WL) pathway and Calvin–Benson–Bassham (CBB) cycle with type III Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO). They could oxidize sulfur, arsenic, and hydrogen, and respire anaerobically via sulfate reduction and denitrification based on genomic evidence. The redundancy of carbon utilizing and element cycling functions, and the interactive processes of syntrophic and sequential utilization of substrates from community-level metabolic prediction, enable wide accessibility of carbon and energy sources to microorganisms. Hydrothermarchaeota members derived important functional components from the community through lateral gene transfer, and became clade-distinctive on genome content, which might serve as a niche-adaptive strategy to metabolize potential heavy metals, C1 compounds, and reduced sulfur compounds.ImportanceThis study provides comprehensive metabolic insights on Hydrothermarchaeota from comparative genomics, evolution and community-level aspects. Hydrothermarchaeota synergistically participates in a wide range of carbon utilizing and element cycling processes with other microbes in the community. We expand the current understanding of community interactions within hydrothermal sediment environments, suggesting that microbial interactions driven by functions are essential to nutrient and element cycling.

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Genome- and Community-Level Interaction Insights into Carbon Utilization and Element Cycling Functions of Hydrothermarchaeota in Hydrothermal Sediment

mSystems ◽

10.1128/msystems.00795-19 ◽

2020 ◽

Vol 5 (1) ◽

Cited By ~ 10

Author(s):

Zhichao Zhou ◽

Yang Liu ◽

Wei Xu ◽

Jie Pan ◽

Zhu-Hua Luo ◽

...

Keyword(s):

Community Level ◽

Data Sets ◽

Carbon Utilization ◽

Black Smoker ◽

Community Interactions ◽

Element Cycling ◽

Bisphosphate Carboxylase ◽

Hydrothermal Sediment ◽

Wide Range ◽

Functional Components

ABSTRACT Hydrothermal vents release reduced compounds and small organic carbon compounds into the surrounding seawater, providing essential substrates for microbial growth and bioenergy transformations. Despite the wide distribution of the marine benthic group E archaea (referred to as Hydrothermarchaeota) in the hydrothermal environment, little is known about their genomic repertoires and biogeochemical significance. Here, we studied four highly complete (>80%) metagenome-assembled genomes (MAGs) from a black smoker chimney and the surrounding sulfur-rich sediments on the South Atlantic Mid-Ocean Ridge and publicly available data sets (the Integrated Microbial Genomes system of the U.S. Department of Energy-Joint Genome Institute and NCBI SRA data sets). Genomic analysis suggested a wide carbon metabolic diversity of Hydrothermarchaeota members, including the utilization of proteins, lactate, and acetate; the anaerobic degradation of aromatics; the oxidation of C1 compounds (CO, formate, and formaldehyde); the utilization of methyl compounds; CO2 incorporation by the tetrahydromethanopterin-based Wood-Ljungdahl pathway; and participation in the type III ribulose-1,5-bisphosphate carboxylase/oxygenase-based Calvin-Benson-Bassham cycle. These microbes also potentially oxidize sulfur, arsenic, and hydrogen and engage in anaerobic respiration based on sulfate reduction and denitrification. Among the 140 MAGs reconstructed from the black smoker chimney microbial community (including Hydrothermarchaeota MAGs), community-level metabolic predictions suggested a redundancy of carbon utilization and element cycling functions and interactive syntrophic and sequential utilization of substrates. These processes might make various carbon and energy sources widely accessible to the microorganisms. Further, the analysis suggested that Hydrothermarchaeota members contained important functional components obtained from the community via lateral gene transfer, becoming a distinctive clade. This might serve as a niche-adaptive strategy for metabolizing heavy metals, C1 compounds, and reduced sulfur compounds. Collectively, the analysis provides comprehensive metabolic insights into the Hydrothermarchaeota. IMPORTANCE This study provides comprehensive metabolic insights into the Hydrothermarchaeota from comparative genomics, evolution, and community-level perspectives. Members of the Hydrothermarchaeota synergistically participate in a wide range of carbon-utilizing and element cycling processes with other microorganisms in the community. We expand the current understanding of community interactions within the hydrothermal sediment and chimney, suggesting that microbial interactions based on sequential substrate metabolism are essential to nutrient and element cycling.

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Secretory Proteases of the Human Skin Microbiome

Infection and Immunity ◽

10.1128/iai.00397-21 ◽

2021 ◽

Author(s):

Wisely Chua ◽

Si En Poh ◽

Hao Li

Keyword(s):

Human Skin ◽

Hydrolytic Enzymes ◽

Microbial Interactions ◽

Skin Microbiome ◽

Protein Cleavage ◽

Wide Range ◽

Range Of Functions ◽

Diverse Community ◽

Secreted Proteases ◽

Pathogenic Agents

The human skin is our outermost layer and serves as a protective barrier against external insults. Advances in next generation sequencing have enabled the discoveries of a rich and diverse community of microbes - bacteria, fungi and viruses that are residents of this surface. The genomes of these microbes also revealed the presence of many secretory enzymes. In particular, proteases which are hydrolytic enzymes capable of protein cleavage and degradation are of special interest in the skin environment which is enriched in proteins and lipids. In this minireview, we will focus on the roles of these skin-relevant microbial secreted proteases, both in terms of their widely studied roles as pathogenic agents in tissue invasion and host immune inactivation, and their recently discovered roles in inter-microbial interactions and modulation of virulence factors. From these studies, it has become apparent that while microbial proteases are capable of a wide range of functions, their expression is tightly regulated and highly responsive to the environments the microbes are in. With the introduction of new biochemical and bioinformatics tools to study protease functions, it will be important to understand the roles played by skin microbial secretory proteases in cutaneous health, especially the less studied commensal microbes with an emphasis on contextual relevance.

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Deciphering the evolution of microbial interactions: in silico studies of two-member microbial communities

10.1101/2022.01.14.476316 ◽

2022 ◽

Author(s):

Gayathri Sambamoorthy ◽

Karthik Raman

Keyword(s):

Microbial Communities ◽

In Silico ◽

Microbial Interactions ◽

Interaction Patterns ◽

Wild Type ◽

Community Function ◽

Evolutionary Forces ◽

In Silico Studies ◽

Wide Range ◽

In The Wild

Microbes thrive in communities, embedded in a complex web of interactions. These interactions, particularly metabolic interactions, play a crucial role in maintaining the community structure and function. As the organisms thrive and evolve, a variety of evolutionary processes alter the interactions among the organisms in the community, although the community function remains intact. In this work, we simulate the evolution of two-member microbial communities in silico to study how evolutionary forces can shape the interactions between organisms. We employ genomescale metabolic models of organisms from the human gut, which exhibit a range of interaction patterns, from mutualism to parasitism. We observe that the evolution of microbial interactions varies depending upon the starting interaction and also on the metabolic capabilities of the organisms in the community. We find that evolutionary constraints play a significant role in shaping the dependencies of organisms in the community. Evolution of microbial communities yields fitness benefits in only a small fraction of the communities, and is also dependent on the interaction type of the wild-type communities. The metabolites cross-fed in the wild-type communities appear in only less than 50% of the evolved communities. A wide range of new metabolites are cross-fed as the communities evolve. Further, the dynamics of microbial interactions are not specific to the interaction of the wild-type community but vary depending on the organisms present in the community. Our approach of evolving microbial communities in silico provides an exciting glimpse of the dynamics of microbial interactions and offers several avenues for future investigations.

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Exploring the Association Between the “Big Five” Personality Traits and Fatal Opioid Overdose: County-Level Empirical Analysis (Preprint)

10.2196/preprints.24939 ◽

2020 ◽

Author(s):

Zhasmina Tacheva ◽

Anton Ivanov

Keyword(s):

United States ◽

Big Five ◽

Psychological Factors ◽

The United States ◽

Community Level ◽

Opioid Overdose ◽

County Level ◽

Psychological Traits ◽

Wide Range ◽

The Relationship

BACKGROUND Opioid-related deaths constitute a problem of pandemic proportions in the United States, with no clear solution in sight. Although addressing addiction—the heart of this problem—ought to remain a priority for health practitioners, examining the community-level psychological factors with a known impact on health behaviors may provide valuable insights for attenuating this health crisis by curbing risky behaviors before they evolve into addiction. OBJECTIVE The goal of this study is twofold: to demonstrate the relationship between community-level psychological traits and fatal opioid overdose both theoretically and empirically, and to provide a blueprint for using social media data to glean these psychological factors in a real-time, reliable, and scalable manner. METHODS We collected annual panel data from Twitter for 2891 counties in the United States between 2014-2016 and used a novel data mining technique to obtain average county-level “Big Five” psychological trait scores. We then performed interval regression, using a control function to alleviate omitted variable bias, to empirically test the relationship between county-level psychological traits and the prevalence of fatal opioid overdoses in each county. RESULTS After controlling for a wide range of community-level biopsychosocial factors related to health outcomes, we found that three of the operationalizations of the five psychological traits examined at the community level in the study were significantly associated with fatal opioid overdoses: extraversion (β=.308, P<.001), neuroticism (β=.248, P<.001), and conscientiousness (β=.229, P<.001). CONCLUSIONS Analyzing the psychological characteristics of a community can be a valuable tool in the local, state, and national fight against the opioid pandemic. Health providers and community health organizations can benefit from this research by evaluating the psychological profile of the communities they serve and assessing the projected risk of fatal opioid overdose based on the relationships our study predict when making decisions for the allocation of overdose-reversal medication and other vital resources.

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Microbial community composition is linked to Sphagnum acclimation to warming

10.5194/egusphere-egu21-13734 ◽

2021 ◽

Author(s):

Tatjana Živković ◽

Alyssa A Carell ◽

Gustaf Granath ◽

Mats B Nilsson ◽

Manuel Helbig ◽

...

Keyword(s):

Growth Rate ◽

Host Plant ◽

Climate Warming ◽

Elevated Temperatures ◽

Critical Role ◽

Temperature Acclimation ◽

Microbial Interactions ◽

Germ Free ◽

Wide Range ◽

Thermal Origin

Peatlands store about third of the terrestrial carbon (C) and exert long-term climate cooling. Dominant plant genera in acidic peatlands, Sphagnum mosses, are main contributors to net primary productivity. Through associative relationships with diverse microbial organisms (microbiome), Sphagnum mosses control major biogeochemical processes, namely uptake, storage and potential release of carbon and nitrogen. Climate warming is expected to negatively impact C accumulation in peatlands and alter nutrient cycling, however Sphagnum-dominated peatland resilience to climate warming may depend on Sphagnum-microbiome associations. The ability of the microbiome to rapidly acclimatize to warming may aid Sphagnum exposed to elevated temperatures through host-microbiome acquired thermotolerance. We investigated the role of the microbiome on Sphagnum&#8217;s ability to acclimate to elevated temperatures using a microbiome-transfer approach to test: a) whether the thermal origin of the microbiome influences acclimation of Sphagnum growth and b) if microbial benefits to Sphagnum growth depend on donor Sphagnum species.&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160; Using a full-factorial design, microbiomes were separated from Sphagnum &#8220;donor&#8221; species from four different peatlands across a wide range of thermal environments (11.4-27&#176;C). The microbiomes were transferred onto germ-free &#8220;recipient&#8221; Sphagnum species in the laboratory and exposed to a range of experimental temperatures (8.5 &#8211; 26.5&#176;C) for growth analysis over 4 weeks.&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160; Normalized growth rates were maximized for plants that received a microbiome from a matched &#8220;donor&#8221; and with a similar origin temperature (&#916;Ttreatment-origin: 0.3&#177;0.9&#176;C [&#177;standard error], p = 0.73). For non-matched &#8220;donor-recipient&#8221; Sphagnum pairs, &#916;Ttreatment-origin was slightly negative with -4.1&#177;2.1&#176;C (p = 0.06). The largest growth rate of the &#8220;recipient&#8221; was measured when grown with a microbiome from a matching &#8220;donor&#8221; Sphagnum species and was 252% and 48% larger than the maximum growth rate of the germ-free Sphagnum and the non-matched &#8220;donor-recipient&#8221; Sphagnum pairs, respectively.&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160; Our results suggest that the composition of the Sphagnum microbiome plays a critical role in host plant temperature acclimation. We found that microbially-provided benefits to the host plant were most pronounced when: 1) the thermal origin of the microbiome is similar to experimental temperatures, and 2) when donor and recipient Sphagnum species are the same. Together, these results suggest that Sphagnum temperature acclimation can be modulated, in part, by microbial interactions and may potentially play a role in peatland resilience to climate warming.

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Disentangling phylogenetic and functional components of shape variation among shoot apical meristems of a wide range of herbaceous angiosperms

American Journal of Botany ◽

10.1002/ajb2.1407 ◽

2019 ◽

Vol 107 (1) ◽

pp. 20-30

Author(s):

Renáta Schnablová ◽

Jiří Neustupa ◽

Kateřina Woodard ◽

Jitka Klimešová ◽

Tomáš Herben

Keyword(s):

Shape Variation ◽

Apical Meristems ◽

Shoot Apical Meristems ◽

Wide Range ◽

Functional Components

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A Toxic Environment: a Growing Understanding of How Microbial Communities Affect Escherichia coli O157:H7 Shiga Toxin Expression

Applied and Environmental Microbiology ◽

10.1128/aem.00509-20 ◽

2020 ◽

Vol 86 (24) ◽

Author(s):

Erin M. Nawrocki ◽

Hillary M. Mosso ◽

Edward G. Dudley

Keyword(s):

Escherichia Coli ◽

Shiga Toxin ◽

Microbial Interactions ◽

Severe Illness ◽

Content Type ◽

E Coli ◽

Wide Range ◽

Lambdoid Prophage

ABSTRACT Enterohemorrhagic Escherichia coli (EHEC) strains, including E. coli O157:H7, cause severe illness in humans due to the production of Shiga toxin (Stx) and other virulence factors. Because Stx is coregulated with lambdoid prophage induction, its expression is especially susceptible to environmental cues. Infections with Stx-producing E. coli can be difficult to model due to the wide range of disease outcomes: some infections are relatively mild, while others have serious complications. Probiotic organisms, members of the gut microbiome, and organic acids can depress Stx production, in many cases by inhibiting the growth of EHEC strains. On the other hand, the factors currently known to amplify Stx act via their effect on the stx-converting phage. Here, we characterize two interactive mechanisms that increase Stx production by O157:H7 strains: first, direct interactions with phage-susceptible E. coli, and second, indirect amplification by secreted factors. Infection of susceptible strains by the stx-converting phage can expand the Stx-producing population in a human or animal host, and phage infection has been shown to modulate virulence in vitro and in vivo. Acellular factors, particularly colicins and microcins, can kill O157:H7 cells but may also trigger Stx expression in the process. Colicins, microcins, and other bacteriocins have diverse cellular targets, and many such molecules remain uncharacterized. The identification of additional Stx-amplifying microbial interactions will improve our understanding of E. coli O157:H7 infections and help elucidate the intricate regulation of pathogenicity in EHEC strains.

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Design, Validation, and Application of a Seven-Strain Staphylococcus aureus PCR Product Microarray for Comparative Genomics

Applied and Environmental Microbiology ◽

10.1128/aem.71.11.7504-7514.2005 ◽

2005 ◽

Vol 71 (11) ◽

pp. 7504-7514 ◽

Cited By ~ 57

Author(s):

Adam A. Witney ◽

Gemma L. Marsden ◽

Matthew T. G. Holden ◽

Richard A. Stabler ◽

Sarah E. Husain ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Comparative Genomics ◽

Microarray Data ◽

Correct Identification ◽

The Novel ◽

Pathogenic Potential ◽

Reading Frame ◽

Pcr Product ◽

Wide Range ◽

Design Build

ABSTRACT Bacterial comparative genomics has been revolutionized by microarrays, but the power of any microarray is dependent on the number and diversity of gene reporters it contains. Staphylococcus aureus is an important human pathogen causing a wide range of invasive and toxin-mediated diseases, and more than 20% of the genome of any isolate consists of variable genes. Seven whole-genome sequences of S. aureus are available, and we exploited this rare opportunity to design, build, and validate a comprehensive, nonredundant PCR product microarray carrying reporters that represent every predicted open reading frame (3,623 probes). Such a comprehensive microarray necessitated a novel design strategy. Validation with the seven sequenced strains showed correct identification of 93.9% of genes present or absent/divergent but was dependent on the method of analysis chosen. Microarray data were highly reproducible, reducing the need for many replicate slides. Interpretation of microarray data was enhanced by focusing on the major areas of variation—the presence or absence of mobile genetic elements (MGEs). We compiled “composite genomes” of every individual MGE and visualized their distribution. This allowed the sensitive discrimination of related isolates, including the first clear description of how isolates of the same clone of epidemic methicillin-resistant S. aureus differ substantially in their carriage of MGEs. These MGEs carry virulence and resistance genes, suggesting differences in pathogenic potential. The novel methods of design and interpretation of data generated from this microarray will enable further studies of S. aureus evolution, epidemiology, and pathogenesis.

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Comparative Genomics of Bacillus species and its Relevance in Industrial Microbiology

Genomics Insights ◽

10.4137/gei.s12732 ◽

2013 ◽

Vol 6 ◽

pp. GEI.S12732 ◽

Cited By ~ 6

Author(s):

Archana Sharma ◽

T. Satyanarayana

Keyword(s):

Comparative Genomics ◽

Molecular Biology ◽

Genome Sequencing ◽

High Throughput Sequencing ◽

Bacterial Species ◽

Bacillus Species ◽

Genome Sequences ◽

Wide Range ◽

Sequencing Platforms ◽

Analytical Tools

With the advent of high throughput sequencing platforms and relevant analytical tools, the rate of microbial genome sequencing has accelerated which has in turn led to better understanding of microbial molecular biology and genetics. The complete genome sequences of important industrial organisms provide opportunities for human health, industry, and the environment. Bacillus species are the dominant workhorses in industrial fermentations. Today, genome sequences of several Bacillus species are available, and comparative genomics of this genus helps in understanding their physiology, biochemistry, and genetics. The genomes of these bacterial species are the sources of many industrially important enzymes and antibiotics and, therefore, provide an opportunity to tailor enzymes with desired properties to suit a wide range of applications. A comparative account of strengths and weaknesses of the different sequencing platforms are also highlighted in the review.

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Soil microbial biomass, community level physiological profiles relate to tree species and its state in urban environment

10.5194/egusphere-egu2020-1064 ◽

2020 ◽

Author(s):

Alexandra Seleznyova ◽

Alexey Yaroslavtcev ◽

Olga Gavrichkova ◽

Alexey Ryazanov ◽

Julia Kovaleva ◽

...

Keyword(s):

Microbial Biomass ◽

Microbial Diversity ◽

Carboxylic Acids ◽

Tree Species ◽

Diversity Index ◽

Soil Microbial Communities ◽

Community Level ◽

Soil Microbial ◽

Vertical Stability ◽

Wide Range

Urban trees and soil microbial communities are the key ecosystem components to provide the supporting, provisioning and regulating services that define citizen&#8217;s well-being. Understanding the relationships between physiological states, age, species of trees and microbial functional properties are needed for a management of urban areas and landscapes' engineering. The research focuses on finding linkages between a wide range of trees&#8217; properties monitored by smart TreeTalker technology and soil functional microbial indexes in Moscow megapolis.The study was carried out on the RUDN University campus area (Moscow, Russia), where six tree species were selected (Pinus sylvestris, Populus tremula, Acer platanoides, Tilia cordata, Picea abies, Betula pendula). TreeTalker device was installed on the preselected five trees of each species for monitoring the sap flux, vertical stability (according to digital accelerometer), spectrums of canopy reflectance, trunk and canopy air temperature and humidity. Monitoring started in May 2019. The composite soil samples (0-10) were taken under each tree at the 0.5 m distance from its stand by augering in October 2019. In the samples, the microbial biomass carbon (MBC, SIR-method), basal respiration (BR), community level physiological profile (CLPP, MicroResp) and Shannon microbial diversity index (H&#8217;) based on CLPP were determined.Soil MBC content was significantly depended on tree species, increasing from A.platanoides to T.cordata (from 538 to 1445 &#181;g C g-1). The microbial diversity index was lowest in soil under A.platanoides (H&#8217;=2.1) and the highest for B.pendula (H&#8217;=2.4). The soil CLPP for A.platanoides was mainly shifted to microbial response on carboxylic acids with the low reaction on amino and phenolic acids compared to other trees species (e.g. B.pendula). Soil qCO2 (BR/MBC ratio) was positively related to trees&#8217; age (r=0.8). Response to carboxylic acids (especially oxalic) had the highest correlation with physiological properties of the trees: trunk moisture, photochemical reflectance index and vertical stability (r > -0.5).Current research was financially supported by Russian Science Foundation [No 19-77-30012].

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