Transitory microbial habitat in the hyperarid Atacama Desert.

Traces of life are nearly ubiquitous on Earth. However, a central unresolved question is whether these traces always indicate an active microbial community or whether, in extreme environments, such as hyperarid deserts, they instead reflect just dormant or dead cells. Although microbial biomass and diversity decrease with increasing aridity in the Atacama Desert, we provide multiple lines of evidence for the presence of an at times metabolically active, microbial community in one of the driest places on Earth. We base this observation on four major lines of evidence: (i) a physico-chemical characterization of the soil habitability after an exceptional rain event, (ii) identified biomolecules indicative of potentially active cells [e.g., presence of ATP, phospholipid fatty acids (PLFAs), metabolites, and enzymatic activity], (iii) measurements of in situ replication rates of genomes of uncultivated bacteria reconstructed from selected samples, and (iv) microbial community patterns specific to soil parameters and depths. We infer that the microbial populations have undergone selection and adaptation in response to their specific soil microenvironment and in particular to the degree of aridity. Collectively, our results highlight that even the hyperarid Atacama Desert can provide a habitable environment for microorganisms that allows them to become metabolically active following an episodic increase in moisture and that once it decreases, so does the activity of the microbiota. These results have implications for the prospect of life on other planets such as Mars, which has transitioned from an earlier wetter environment to today's extreme hyperaridity.

The metagenomic landscape of xenobiotics biodegradation in mangrove sediments.

Metagenomics is a powerful approach to study microorganisms present in any given environment and their potential to maintain and improve ecosystem health without the need of cultivating these microorganisms in the laboratory. In this study, we combined a cultivation-independent metagenomics approach with functional assays to identify the detoxification potential of microbial genes evaluating their potential to contribute to xenobiotics resistance in oil-impacted mangrove sediments. A metagenomic fosmid library containing 12,960 clones from highly contaminated mangrove sediment was used in this study. For assessment of metal resistance, clones were grown in culture medium with increasing concentrations of mercury. The analyses metagenomic library sequences revealed the presence of genes related to heavy metals and antibiotics resistance in the oil-impacted mangrove microbiome. The taxonomic profiling of these sequences suggests that at the genus level, Geobacter was the most abundant genus in our dataset. A functional screening assessment of the metagenomic library successfully detected 24 potential heavy metal tolerant clones, six of which were capable of growing with increased concentrations of mercury. The genetic characterization of selected clones allowed the detection of genes related to detoxification processes, such as chromate transport protein ChrA, haloacid dehalogenase-like hydrolase, lipopolysaccharide transport system, and 3-oxoacyl-[acyl-carrier-protein] reductase. Clones were capable of growing in medium containing increased concentrations of metals and antibiotics, but none manifested strong mercury removal from culture medium characteristic of mercuric reductase activity. These results suggest that resistance to xenobiotic stress varies greatly and that additional studies to elucidate the potential of metal biotransformation need to be carried out with the goal of improving bioremediation application.

Microbial functional responses to long-term anthropogenic impact in mangrove soils.

Mangroves are coastal ecosystems of transition between terrestrial and marine environments, that have been particularly contaminated in the last decades. Organic compounds are part of these contaminants, which have increased in the environment due to industrial activities and accidental oil spills. These contaminants are toxic to higher organisms, but microorganisms can metabolize most of these compounds and thus offer a tool for bioremediation purposes. The aim of the present study was to characterize the microbial potential and activity for degradation of aromatic compounds in sediment samples from mangroves using metagenomic and metatranscriptomic approaches. Sediment samples were collected for DNA and RNA extraction from each of the mangrove sites: highly oil-impacted (Oil Mgv), anthropogenically impacted (Ant Mgv) and pristine (Prs Mgv) mangrove. Hydrocarbon concentrations in Oil Mgv sediments were higher than those observed in Ant Mgv and Prs Mgv. Genes and transcripts associated with aromatic compound degradation, particularly the meta and ortho-pathways, were more abundant in Oil Mgv and Ant Mgv suggesting that many of the aromatic compounds are being aerobically degraded by the microbiome in these sites. Functions involved in the degradation of aromatic compounds were also found in pristine site, although in lower abundance. Members of the genera Aromatoleum, Desulfococcus, Desulfatibacillum, Desulfitobacterium and Vibrio were actively involved in the detoxification of sediments affected by the oil spill. Results obtained from this study provided strong evidence that microbial degradation of aromatic compounds plays an active role in the biological response to mangrove sediment pollution and subsequent ecosystem recovery.

Elviz - exploration of metagenome assemblies with an interactive visualization tool.

BACKGROUND: Metagenomics, the sequencing of DNA collected from an entire microbial community, enables the study of natural microbial consortia in their native habitats. Metagenomics studies produce huge volumes of data, including both the sequences themselves and metadata describing their abundance, assembly, predicted functional characteristics and environmental parameters. The ability to explore these data visually is critically important to meaningful biological interpretation. Current genomics applications cannot effectively integrate sequence data, assembly metadata, and annotation to support both genome and community-level inquiry. RESULTS: Elviz (Environmental Laboratory Visualization) is an interactive web-based tool for the visual exploration of assembled metagenomes and their complex metadata. Elviz allows scientists to navigate metagenome assemblies across multiple dimensions and scales, plotting parameters such as GC content, relative abundance, phylogenetic affiliation and assembled contig length. Furthermore Elviz enables interactive exploration using real-time plot navigation, search, filters, axis selection, and the ability to drill from a whole-community profile down to individual gene annotations. Thus scientists engage in a rapid feedback loop of visual pattern identification, hypothesis generation, and hypothesis testing. CONCLUSIONS: Compared to the current alternative of generating a succession of static figures, Elviz can greatly accelerate the speed of metagenome analysis. Elviz can be used to explore both user-submitted datasets and numerous metagenome studies publicly available at the Joint Genome Institute (JGI). Elviz is freely available at http://genome.jgi.doe.gov/viz and runs on most current web-browsers.

The United States Culture Collection Network (USCCN): Enhancing Microbial Genomics Research through Living Microbe Culture Collections.

The mission of the United States Culture Collection Network (USCCN; http://usccn.org) is "to facilitate the safe and responsible utilization of microbial resources for research, education, industry, medicine, and agriculture for the betterment of human kind." Microbial culture collections are a key component of life science research, biotechnology, and emerging global biobased economies. Representatives and users of several microbial culture collections from the United States and Europe gathered at the University of California, Davis, to discuss how collections of microorganisms can better serve users and stakeholders and to showcase existing resources available in public culture collections.

Identification of novel biomass-degrading enzymes from genomic dark matter: Populating genomic sequence space with functional annotation.

Although recent nucleotide sequencing technologies have significantly enhanced our understanding of microbial genomes, the function of ∼35% of genes identified in a genome currently remains unknown. To improve the understanding of microbial genomes and consequently of microbial processes it will be crucial to assign a function to this "genomic dark matter." Due to the urgent need for additional carbohydrate-active enzymes for improved production of transportation fuels from lignocellulosic biomass, we screened the genomes of more than 5,500 microorganisms for hypothetical proteins that are located in the proximity of already known cellulases. We identified, synthesized and expressed a total of 17 putative cellulase genes with insufficient sequence similarity to currently known cellulases to be identified as such using traditional sequence annotation techniques that rely on significant sequence similarity. The recombinant proteins of the newly identified putative cellulases were subjected to enzymatic activity assays to verify their hydrolytic activity towards cellulose and lignocellulosic biomass. Eleven (65%) of the tested enzymes had significant activity towards at least one of the substrates. This high success rate highlights that a gene context-based approach can be used to assign function to genes that are otherwise categorized as "genomic dark matter" and to identify biomass-degrading enzymes that have little sequence similarity to already known cellulases. The ability to assign function to genes that have no related sequence representatives with functional annotation will be important to enhance our understanding of microbial processes and to identify microbial proteins for a wide range of applications.

Estimating geographic variation of infection fatality ratios during epidemics.

Objectives: We aim to estimate geographic variability in total numbers of infections and infection fatality ratios (IFR; the number of deaths caused by an infection per 1,000 infected people) when the availability and quality of data on disease burden are limited during an epidemic. Methods: We develop a noncentral hypergeometric framework that accounts for differential probabilities of positive tests and reflects the fact that symptomatic people are more likely to seek testing. We demonstrate the robustness, accuracy, and precision of this framework, and apply it to the United States (U.S.) COVID-19 pandemic to estimate county-level SARS-CoV-2 IFRs. Results: The estimators for the numbers of infections and IFRs showed high accuracy and precision; for instance, when applied to simulated validation data sets, across counties, Pearson correlation coefficients between estimator means and true values were 0.996 and 0.928, respectively, and they showed strong robustness to model misspecification. Applying the county-level estimators to the real, unsimulated COVID-19 data spanning April 1, 2020 to September 30, 2020 from across the U.S., we found that IFRs varied from 0 to 44.69, with a standard deviation of 3.55 and a median of 2.14. Conclusions: The proposed estimation framework can be used to identify geographic variation in IFRs across settings.

Biochemical characterization of Fsa16295Glu from "Fervidibacter sacchari," the first hyperthermophilic GH50 with ß-1,3-endoglucanase activity and founding member of the subfamily GH50_3.

The aerobic hyperthermophile "Fervidibacter sacchari" catabolizes diverse polysaccharides and is the only cultivated member of the class "Fervidibacteria" within the phylum Armatimonadota. It encodes 117 putative glycoside hydrolases (GHs), including two from GH family 50 (GH50). In this study, we expressed, purified, and functionally characterized one of these GH50 enzymes, Fsa16295Glu. We show that Fsa16295Glu is a ß-1,3-endoglucanase with optimal activity on carboxymethyl curdlan (CM-curdlan) and only weak agarase activity, despite most GH50 enzymes being described as ß-agarases. The purified enzyme has a wide temperature range of 4-95°C (optimal 80°C), making it the first characterized hyperthermophilic representative of GH50. The enzyme is also active at a broad pH range of at least 5.5-11 (optimal 6.5-10). Fsa16295Glu possesses a relatively high kcat/KM of 1.82 × 107 s-1 M-1 with CM-curdlan and degrades CM-curdlan nearly completely to sugar monomers, indicating preferential hydrolysis of glucans containing ß-1,3 linkages. Finally, a phylogenetic analysis of Fsa16295Glu and all other GH50 enzymes revealed that Fsa16295Glu is distant from other characterized enzymes but phylogenetically related to enzymes from thermophilic archaea that were likely acquired horizontally from "Fervidibacteria." Given its functional and phylogenetic novelty, we propose that Fsa16295Glu represents a new enzyme subfamily, GH50_3.

Microbial-Derived Tryptophan Metabolites and Their Role in Neurological Disease: Anthranilic Acid and Anthranilic Acid Derivatives.

The gut microbiome provides the host access to otherwise indigestible nutrients, which are often further metabolized by the microbiome into bioactive components. The gut microbiome can also shift the balance of host-produced compounds, which may alter host health. One precursor to bioactive metabolites is the essential aromatic amino acid tryptophan. Tryptophan is mostly shunted into the kynurenine pathway but is also the primary metabolite for serotonin production and the bacterial indole pathway. Balance between tryptophan-derived bioactive metabolites is crucial for neurological homeostasis and metabolic imbalance can trigger or exacerbate neurological diseases. Alzheimer's, depression, and schizophrenia have been linked to diverging levels of tryptophan-derived anthranilic, kynurenic, and quinolinic acid. Anthranilic acid from collective microbiome metabolism plays a complex but important role in systemic host health. Although anthranilic acid and its metabolic products are of great importance for host-microbe interaction in neurological health, literature examining the mechanistic relationships between microbial production, host regulation, and neurological diseases is scarce and at times conflicting. This narrative review provides an overview of the current understanding of anthranilic acid's role in neurological health and disease, with particular focus on the contribution of the gut microbiome, the gut-brain axis, and the involvement of the three major tryptophan pathways.

Salmonella enhances osteogenic differentiation in adipose-derived mesenchymal stem cells.

The potential of mesenchymal stem cells (MSCs) for tissue repair and regeneration has garnered great attention. While MSCs are likely to interact with microbes at sites of tissue damage and inflammation, like in the gastrointestinal system, the consequences of pathogenic association on MSC activities have yet to be elucidated. This study investigated the effects of pathogenic interaction on MSC trilineage differentiation paths and mechanisms using model intracellular pathogen Salmonella enterica ssp enterica serotype Typhimurium. The examination of key markers of differentiation, apoptosis, and immunomodulation demonstrated that Salmonella altered osteogenic and chondrogenic differentiation pathways in human and goat adipose-derived MSCs. Anti-apoptotic and pro-proliferative responses were also significantly upregulated (p < 0.05) in MSCs during Salmonella challenge. These results together indicate that Salmonella, and potentially other pathogenic bacteria, can induce pathways that influence both apoptotic response and functional differentiation trajectories in MSCs, highlighting that microbes have a potentially significant role as influencers of MSC physiology and immune activity.

Two-component systems regulate bacterial virulence in response to the host gastrointestinal environment and metabolic cues.

Two-component systems are ubiquitous signaling mechanisms in bacteria that enable intracellular changes from extracellular cues. These bacterial regulatory systems couple external stimuli to control genetic expression via an autophosphorylation cascade that transduces membrane signals to intracellular locations, thereby allowing bacteria to rapidly adapt to the changing environmental conditions. Well known to control basic cellular processes, it is evident that two-component systems also exercise control over virulence traits, such as motility, secretion systems, and stress responses that impact the complex cascade of networks that alter virulence traits. In the gastrointestinal system, cues for activation of virulence-related two-component systems include metal ions, host-derived metabolites, and gut conditions. The diversity and origin of these cues suggest that the host can exert control over enteric pathogenicity via regulation in the gastrointestinal system. With the rise in multi-drug resistant pathogens, the potential control of pathogenicity with host cues via two-component systems presents a potential alternative to antimicrobials. Though the signaling mechanism itself is well studied, to date there is no systematic review compiling the host-associated cues of two-component systems and virulence traits. This review highlights the direct link between the host gastrointestinal environment and pathogenicity by focusing on two-component systems that are associated with the genetic expression of virulence traits, and that are activated by host-derived cues. The direct link between the host gastrointestinal environment, metabolites, and pathogenicity established in this review both underscores the importance of host-derived cues on bacterial activity and presents an enticing therapeutic target in the fight against antimicrobial resistant pathogens.

Impact of Probiotics on Dairy Production Efficiency.

There has been growing interest on probiotics to enhance weight gain and disease resistance in young calves and to improve the milk yield in lactating animals by reducing the negative energy balance during the peak lactation period. While it has been well established that probiotics modulate the microbial community composition in the gastrointestinal tract, and a probiotic-mediated homeostasis in the rumen could improve feed conversation competence, volatile fatty acid production and nitrogen flow that enhances the milk composition as well as milk production, detailed changes on the molecular and metabolic level prompted by probiotic feed additives are still not understood. Moreover, as living biotherapeutic agents, probiotics have the potential to directly change the gene expression profile of animals by activating the signalling cascade in the host cells. Various direct and indirect components of probiotic approaches to improve the productivity of dairy animals are discussed in this review.

In silico identification of two peptides with antibacterial activity against multidrug-resistant Staphylococcus aureus.

Here we report two antimicrobial peptides (AMPs), HG2 and HG4 identified from a rumen microbiome metagenomic dataset, with activity against multidrug-resistant (MDR) bacteria, especially methicillin-resistant Staphylococcus aureus (MRSA) strains, a major hospital and community-acquired pathogen. We employed the classifier model design to analyse, visualise, and interpret AMP activities. This approach allowed in silico discrimination of promising lead AMP candidates for experimental evaluation. The lead AMPs, HG2 and HG4, are fast-acting and show anti-biofilm and anti-inflammatory activities in vitro and demonstrated little toxicity to human primary cell lines. The peptides were effective in vivo within a Galleria mellonella model of MRSA USA300 infection. In terms of mechanism of action, HG2 and HG4 appear to interact with the cytoplasmic membrane of target cells and may inhibit other cellular processes, whilst preferentially binding to bacterial lipids over human cell lipids. Therefore, these AMPs may offer additional therapeutic templates for MDR bacterial infections.

Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages.

Microbial sulfur metabolism contributes to biogeochemical cycling on global scales. Sulfur metabolizing microbes are infected by phages that can encode auxiliary metabolic genes (AMGs) to alter sulfur metabolism within host cells but remain poorly characterized. Here we identified 191 phages derived from twelve environments that encoded 227 AMGs for oxidation of sulfur and thiosulfate (dsrA, dsrC/tusE, soxC, soxD and soxYZ). Evidence for retention of AMGs during niche-differentiation of diverse phage populations provided evidence that auxiliary metabolism imparts measurable fitness benefits to phages with ramifications for ecosystem biogeochemistry. Gene abundance and expression profiles of AMGs suggested significant contributions by phages to sulfur and thiosulfate oxidation in freshwater lakes and oceans, and a sensitive response to changing sulfur concentrations in hydrothermal environments. Overall, our study provides fundamental insights on the distribution, diversity, and ecology of phage auxiliary metabolism associated with sulfur and reinforces the necessity of incorporating viral contributions into biogeochemical configurations.

Ecology and molecular targets of hypermutation in the global microbiome.

Changes in the sequence of an organism's genome, i.e., mutations, are the raw material of evolution. The frequency and location of mutations can be constrained by specific molecular mechanisms, such as diversity-generating retroelements (DGRs). DGRs have been characterized from cultivated bacteria and bacteriophages, and perform error-prone reverse transcription leading to mutations being introduced in specific target genes. DGR loci were also identified in several metagenomes, but the ecological roles and evolutionary drivers of these DGRs remain poorly understood. Here, we analyze a dataset of >30,000 DGRs from public metagenomes, establish six major lineages of DGRs including three primarily encoded by phages and seemingly used to diversify host attachment proteins, and demonstrate that DGRs are broadly active and responsible for >10% of all amino acid changes in some organisms. Overall, these results highlight the constraints under which DGRs evolve, and elucidate several distinct roles these elements play in natural communities.

Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber.

The rumen harbors a complex microbial mixture of archaea, bacteria, protozoa, and fungi that efficiently breakdown plant biomass and its complex dietary carbohydrates into soluble sugars that can be fermented and subsequently converted into metabolites and nutrients utilized by the host animal. While rumen bacterial populations have been well documented, only a fraction of the rumen eukarya are taxonomically and functionally characterized, despite the recognition that they contribute to the cellulolytic phenotype of the rumen microbiota. To investigate how anaerobic fungi actively engage in digestion of recalcitrant fiber that is resistant to degradation, we resolved genome-centric metaproteome and metatranscriptome datasets generated from switchgrass samples incubated for 48 h in nylon bags within the rumen of cannulated dairy cows. Across a gene catalog covering anaerobic rumen bacteria, fungi and viruses, a significant portion of the detected proteins originated from fungal populations. Intriguingly, the carbohydrate-active enzyme (CAZyme) profile suggested a domain-specific functional specialization, with bacterial populations primarily engaged in the degradation of hemicelluloses, whereas fungi were inferred to target recalcitrant cellulose structures via the detection of a number of endo- and exo-acting enzymes belonging to the glycoside hydrolase (GH) family 5, 6, 8, and 48. Notably, members of the GH48 family were amongst the highest abundant CAZymes and detected representatives from this family also included dockerin domains that are associated with fungal cellulosomes. A eukaryote-selected metatranscriptome further reinforced the contribution of uncultured fungi in the ruminal degradation of recalcitrant fibers. These findings elucidate the intricate networks of in situ recalcitrant fiber deconstruction, and importantly, suggest that the anaerobic rumen fungi contribute a specific set of CAZymes that complement the enzyme repertoire provided by the specialized plant cell wall degrading rumen bacteria.

Anaerobic Fungi: Past, Present, and Future.

Anaerobic fungi (AF) play an essential role in feed conversion due to their potent fiber degrading enzymes and invasive growth. Much has been learned about this unusual fungal phylum since the paradigm shifting work of Colin Orpin in the 1970s, when he characterized the first AF. Molecular approaches targeting specific phylogenetic marker genes have facilitated taxonomic classification of AF, which had been previously been complicated by the complex life cycles and associated morphologies. Although we now have a much better understanding of their diversity, it is believed that there are still numerous genera of AF that remain to be described in gut ecosystems. Recent marker-gene based studies have shown that fungal diversity in the herbivore gut is much like the bacterial population, driven by host phylogeny, host genetics and diet. Since AF are major contributors to the degradation of plant material ingested by the host animal, it is understandable that there has been great interest in exploring the enzymatic repertoire of these microorganisms in order to establish a better understanding of how AF, and their enzymes, can be used to improve host health and performance, while simultaneously reducing the ecological footprint of the livestock industry. A detailed understanding of AF and their interaction with other gut microbes as well as the host animal is essential, especially when production of affordable high-quality protein and other animal-based products needs to meet the demands of an increasing human population. Such a mechanistic understanding, leading to more sustainable livestock practices, will be possible with recently developed -omics technologies that have already provided first insights into the different contributions of the fungal and bacterial population in the rumen during plant cell wall hydrolysis.

Phototrophic Co-cultures From Extreme Environments: Community Structure and Potential Value for Fundamental and Applied Research.

Cyanobacteria are found in most illuminated environments and are key players in global carbon and nitrogen cycling. Although significant efforts have been made to advance our understanding of this important phylum, still little is known about how members of the cyanobacteria affect and respond to changes in complex biological systems. This lack of knowledge is in part due to our dependence on pure cultures when determining the metabolism and function of a microorganism. We took advantage of the Culture Collection of Microorganisms from Extreme Environments (CCMEE), a collection of more than 1,000 publicly available photosynthetic co-cultures maintained at the Pacific Northwest National Laboratory, and assessed via 16S rRNA amplicon sequencing if samples readily available from public culture collection could be used in the future to generate new insights into the role of microbial communities in global and local carbon and nitrogen cycling. Results from this work support the existing notion that culture depositories in general hold the potential to advance fundamental and applied research. Although it remains to be seen if co-cultures can be used at large scale to infer roles of individual organisms, samples that are publicly available from existing co-cultures depositories, such as the CCMEE, might be an economical starting point for such studies. Access to archived biological samples, without the need for costly field work, might in some circumstances be one of the few remaining ways to advance the field and to generate new insights into the biology of ecosystems that are not easily accessible. The current COVID-19 pandemic, which makes sampling expeditions almost impossible without putting the health of the participating scientists on the line, is a very timely example.

Key Considerations for the Use of Seaweed to Reduce Enteric Methane Emissions From Cattle.

Enteric methane emissions are the single largest source of direct greenhouse gas emissions (GHG) in beef and dairy value chains and a substantial contributor to anthropogenic methane emissions globally. In late 2019, the World Wildlife Fund (WWF), the Advanced Research Projects Agency-Energy (ARPA-E) and the Foundation for Food and Agriculture Research (FFAR) convened approximately 50 stakeholders representing research and production of seaweeds, animal feeds, dairy cattle, and beef and dairy foods to discuss challenges and opportunities associated with the use of seaweed-based ingredients to reduce enteric methane emissions. This Perspective article describes the considerations identified by the workshop participants and suggests next steps for the further development and evaluation of seaweed-based feed ingredients as enteric methane mitigants. Although numerous compounds derived from sources other than seaweed have been identified as having enteric methane mitigation potential, these mitigants are outside the scope of this article.