Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater

AbstractWhile oligotrophic deep groundwaters host active microbes attuned to the low-end of the bioenergetics spectrum, the ecological constraints on microbial niches in these ecosystems and their consequences for microbiome convergence are unknown. Here, we provide a genome-resolved, integrated omics analysis comparing archaeal and bacterial communities in disconnected fracture fluids of the Fennoscandian Shield in Europe. Leveraging a dataset that combines metagenomes, single cell genomes, and metatranscriptomes, we show that groundwaters flowing in similar lithologies offer fixed niches that are occupied by a common core microbiome. Functional expression analysis highlights that these deep groundwater ecosystems foster diverse, yet cooperative communities adapted to this setting. We suggest that these communities stimulate cooperation by expression of functions related to ecological traits, such as aggregate or biofilm formation, while alleviating the burden on microorganisms producing compounds or functions that provide a collective benefit by facilitating reciprocal promiscuous metabolic partnerships with other members of the community. We hypothesize that an episodic lifestyle enabled by reversible bacteriostatic functions ensures the subsistence of the oligotrophic deep groundwater microbiome.

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Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater

10.1101/2020.05.24.111179 ◽

2020 ◽

Author(s):

Maliheh Mehrshad ◽

Margarita Lopez-Fernandez ◽

John Sundh ◽

Emma Bell ◽

Domenico Simone ◽

...

Keyword(s):

Functional Expression ◽

Primary Energy ◽

Biological Interactions ◽

Way Of Life ◽

Deep Groundwater ◽

Core Microbiome ◽

Niche Shifts ◽

Groundwater Ecosystems ◽

Domains Of Life ◽

Underlying Mechanisms

AbstractExtremely oligotrophic deep groundwaters host organisms attuned to the low-end of the bioenergetics spectrum. While all domains of life along with viruses are active in this habitat, the evolutionary and ecological constraints on colonization and niche shifts and their consequences for the microbiome convergence are unknown. Here we provide a comparative genome-resolved analysis of the prokaryotic community in disconnected fracture fluids of the Fennoscandian Shield. The data show that the oligotrophic deep groundwaters flowing in similar lithologies offer fixed niches that are occupied by a common deep groundwater core microbiome. Based on this high resolution “multi-omics” enabled understanding of the underlying mechanisms via functional expression analysis, we conclude that deep groundwater ecosystems foster highly diverse, yet cooperative microbial communities adapted to this setting. The fitness of primary energy producers is increased by ecological traits such as aggregate or biofilm formation. This also facilitates reciprocal promiscuous partnerships with diverse and prevalent epi-bionts, alleviating the “tragedy of common goods”. Hence, instead of a lifestyle where microbes predominantly invest in functions related to maintenance and survival, an episodic and cooperative lifestyle ensures the subsistence of the deep groundwater microbiome. We suggest the name “halt and catch fire” for this way of life.

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Integrated Omics Strategy Reveals Cyclic Lipopeptides Empedopeptins from Massilia sp. YMA4 and Their Biosynthetic Pathway

Marine Drugs ◽

10.3390/md19040209 ◽

2021 ◽

Vol 19 (4) ◽

pp. 209

Author(s):

Shang-Tse Ho ◽

Ying-Ning Ho ◽

Chih Lin ◽

Wei-Chen Hsu ◽

Han-Jung Lee ◽

...

Keyword(s):

Amino Acid ◽

Antibiotic Activity ◽

Bioactive Metabolites ◽

Null Mutant ◽

Bacterial Strains ◽

Isolation And Purification ◽

Cyclic Lipopeptides ◽

A Genome ◽

Mutant Strains ◽

Integrated Omics

Empedopeptins—eight amino acid cyclic lipopeptides—are calcium-dependent antibiotics that act against Gram-positive bacteria such as Staphylococcus aureus by inhibiting cell wall biosynthesis. However, to date, the biosynthetic mechanism of the empedopeptins has not been well identified. Through comparative genomics and metabolomics analysis, we identified empedopeptin and its new analogs from a marine bacterium, Massilia sp. YMA4. We then unveiled the empedopeptin biosynthetic gene cluster. The core nonribosomal peptide gene null-mutant strains (ΔempC, ΔempD, and ΔempE) could not produce empedopeptin, while dioxygenase gene null-mutant strains (ΔempA and ΔempB) produced several unique empedopeptin analogs. However, the antibiotic activity of ΔempA and ΔempB was significantly reduced compared with the wild-type, demonstrating that the hydroxylated amino acid residues of empedopeptin and its analogs are important to their antibiotic activity. Furthermore, we found seven bacterial strains that could produce empedopeptin-like cyclic lipopeptides using a genome mining approach. In summary, this study demonstrated that an integrated omics strategy can facilitate the discovery of potential bioactive metabolites from microbial sources without further isolation and purification.

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High dimensional geometry of fitness landscapes identifies master regulators of evolution and the microbiome

10.1101/2021.09.11.459926 ◽

2021 ◽

Author(s):

Holger Eble ◽

Michael Joswig ◽

Lisa Lamberti ◽

William B. Ludington

Keyword(s):

Fitness Landscape ◽

Probiotic Bacterium ◽

High Dimensional ◽

Biological Interactions ◽

Local Optima ◽

Ecological Diversification ◽

A Genome ◽

Wide Scale ◽

Key Genes ◽

The Individual

A longstanding goal of biology is to identify the key genes and species that critically impact evolution, ecology, and health. Yet biological interactions between genes (1, 2), species (3–6), and different environmental contexts (7–9) change the individual effects due to non-additive interactions, known as epistasis. In the fitness landscape concept, each gene/organism/environment is modeled as a separate biological dimension (10), yielding a high dimensional landscape, with epistasis adding local peaks and valleys to the landscape. Massive efforts have defined dense epistasis networks on a genome-wide scale (2), but these have mostly been limited to pairwise, or two-dimensional, interactions (11). Here we develop a new mathematical formalism that allows us to quantify interactions at high dimensionality in genetics and the microbiome. We then generate and also reanalyze combinatorically complete datasets (two genetic, two microbiome). In higher dimensions, we find that key genes (e.g. pykF) and species (e.g. Lactobacillus plantarum) distort the fitness landscape, changing the interactions for many other genes/species. These distortions can fracture a “smooth” landscape with one optimal fitness peak into a landscape with many local optima, regulating evolutionary or ecological diversification (12), which may explain how a probiotic bacterium can stabilize the gut microbiome.

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Characteristics of Ruminal Microbial Community: Evolutionary and Ecological Perspectives

10.20944/preprints202012.0628.v1 ◽

2020 ◽

Author(s):

Amlan Kumar Patra

Keyword(s):

Microbial Community ◽

Ruminal Fermentation ◽

Plant Leaves ◽

Ecological Traits ◽

Core Microbiome ◽

Core Microbiota ◽

The Core ◽

Ruminant Species ◽

Ruminal Microbiota ◽

Evolutionary Perspectives

Ruminants perhaps appeared about 50 million years ago (Ma). Five ruminant families had been extinct and about 200 species in 6 ruminant families are living today. The first ruminant family probably was small omnivore without functional ruminal microbiota to digest fiber. Subsequently, other ruminant families evolved around 18-23 Ma along with woodlands and grasslands. Probably, ruminants started to consume selective and highly nutritious plant leaves and grasses similar to concentrates. By 5-11 Ma, grasslands expanded and some ruminants used more grass in their diets with comparatively low nutritive values and high fibers. Historically, humans have domesticated 9 ruminant species that are mostly utilizer of low quality forages for human benefits. Thus, the non-functional rumen microbiota to predominantly concentrate fermenting microbiota, followed by predominantly fiber digesting microbiota had evolved for mutual complementary benefits of holobiont over the million years. The core microbiome of ruminant species seems the resultant of hologenome interaction in an evolutionary unit. The inertia and resilience properties of ruminal ecosystem seem to be due to this core microbiota, which makes the ecosystem most stable in response to perturbations because this core microbiota has evolutionary advantages with logically more generalists (i.e., wide metabolic versatile and redundancy). Also, a part of the ruminal microbiome shows highly plasticity, which is likely useful for evolutionary adaptability of holobiont. This review discusses ecological characteristics of ruminal microbial community in evolutionary perspectives. The updated understanding of ecological traits of ruminal microbiome would be helpful to better modulate the ruminal fermentation favorably for human benefits.

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Isoforms of SLC26A6 mediate anion transport and have functional PDZ interaction domains

AJP Cell Physiology ◽

10.1152/ajpcell.00270.2002 ◽

2003 ◽

Vol 284 (3) ◽

pp. C769-C779 ◽

Cited By ~ 95

Author(s):

Hannes Lohi ◽

Georg Lamprecht ◽

Daniel Markovich ◽

Anders Heil ◽

Minna Kujala ◽

...

Keyword(s):

Splice Variants ◽

Functional Characterization ◽

Regulatory Protein ◽

Functional Expression ◽

General Concept ◽

Specific Gene ◽

Anion Transporters ◽

A Genome ◽

Alternatively Spliced

The solute carrier gene family SLC26 consists of tissue-specific anion exchanger genes, three of them associated with distinct human recessive disorders. By a genome-driven approach, several new SLC26 family members have been identified, including a kidney- and pancreas-specific gene, SLC26A6. We report the functional characterization of SLC26A6 and two new alternatively spliced variants, named SLC26A6c and SLC26A6d. Immunofluorescence studies on transiently transfected cells indicated membrane localization and indicated that both NH2- and COOH-terminal tails of the SLC26A6 variants are located intracellularly, suggesting a topology with an even number of transmembrane domains. Functional expression of the three proteins in Xenopus oocytes demonstrated Cl− and SO[Formula: see text] transport activity. In addition, the transport of SO[Formula: see text] and Cl− was inhibited by DIDS and HCO[Formula: see text]. We demonstrated also that the COOH terminus of SLC26A6 binds to the first and second PDZ domains of the Na+/H+ exchanger (NHE)3 kinase A regulatory protein (E3KARP) and NHE3 regulatory factor (NHERF) proteins in vitro. Truncation of the last three amino acids (TRL) of SLC26A6 abrogated the interaction but did not affect transport function. These results demonstrate that SLC26A6 and its two splice variants can function as anion transporters linked to PDZ-interaction pathways. Our results support the general concept of microdomain organization for ion transport and suggest a mechanism for cystic fibrosis transmembrane regulator (CFTR)-mediated SLC26A6 upregulation in pancreatic duct cells.

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Temporal environmental variation imposes differential selection on genomic and ecological traits of virtual plant communities

10.1101/2020.03.24.005058 ◽

2020 ◽

Cited By ~ 1

Author(s):

Ludwig Leidinger ◽

Juliano Sarmento Cabral

Keyword(s):

Temporal Variation ◽

Plant Communities ◽

Species Turnover ◽

Environmental Variation ◽

Life Cycles ◽

Ecological Traits ◽

Virtual Plant ◽

Standing Variation ◽

Variable Environments ◽

A Genome

AbstractThe reaction of species to changing conditions determines how community composition will change functionally — not only by (temporal) species turnover, but also by trait shifts within species. For the latter, selection from standing variation has been suggested to be more efficient than acquiring new mutations. Yet, studies on community trait composition and trait selection largely focus on phenotypic variation in ecological traits, whereas the underlying genomic traits remain relatively understudied despite evidence of their role to standing variation. Using a genome-explicit, niche- and individual-based model, we address the potential interactions between genomic and ecological traits shaping communities under an environmental selective forcing, namely temporal variation. In this model, all ecological traits are explicitly coded by the genome. For our experiments, we initialized 90 replicate communities, each with ca. 350 initial species, characterized by random genomic and ecological trait combinations, on a 2D spatially-explicit landscape with two orthogonal gradients (temperature and resource use). We exposed each community to two contrasting scenarios: without (i.e. static environments) and with temporal variation. We then analyzed emerging compositions of both genomic and ecological traits at the community, population and genomic levels. Communities in variable environments were species poorer than in static environments, populations more abundant and genomes had a higher numbers of genes. The surviving genomes (i.e. those selected by variable environments) coded for enhanced environmental tolerance and smaller biomass, which resulted in faster life cycles and thus also in increased potential for evolutionary rescue. Even under the constant environmental filtering presented by temporal environmental variation, larger, more linked genomes allowed selection of increased variation in dispersal abilities. Our results provide clues to how sexually-reproducing diploid plant communities might react to increased environmental variation and highlights the importance of genomic traits and their interaction with ecological traits for eco-evolutionary responses to changing climates.

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