Genetic diversity in terrestrial subsurface ecosystems impacted by geological degassing

Earth’s mantle releases 38.7 ± 2.9 Tg/yr CO2 along with other reduced and oxidized gases to the atmosphere shaping microbial metabolism at volcanic sites across the globe, yet little is known about its impact on microbial life under non-thermal conditions. Here, we perform comparative metagenomics coupled to geochemical measurements of deep subsurface fluids from a cold-water geyser driven by mantle degassing. Key organisms belonging to uncultivated Candidatus Altiarchaeum show a global biogeographic pattern and site-specific adaptations shaped by gene loss and inter-kingdom horizontal gene transfer. Comparison of the geyser community to 16 other publicly available deep subsurface sites demonstrate a conservation of chemolithoautotrophic metabolism across sites. In silico replication measures suggest a linear relationship of bacterial replication with ecosystems depth with the exception of impacted sites, which show near surface characteristics. Our results suggest that subsurface ecosystems affected by geological degassing are hotspots for microbial life in the deep biosphere.

Metagenomics-Guided Assessment of Water Quality and Predicting Pathogenic Load

Antibiotic-resistant bacteria (ARB) are becoming more prevalent in the environment and are efficiently disseminating through contaminated wastewater resulting in resistome cycling. This chapter compares the bacterial profile of hospital effluents collected from rural, urban, and delta regions of West Bengal, India. Comparative metagenomics analysis identified pathogenic bacterial genera like pseudomonas, escherichia, staphylococcus, lactobacillus, prevotella, acinetobacter across the samples. Delta sample showed highest abundance of pseudomonas whereas rural sample had lower titre of all the common bacterial genera. Urban sample reflected more diversity of different genera in terms of abundance. Pathogenic load prediction revealed significant occurrence of diarrhea, irritable bowel syndrome, liver cirrhosis, ulcerative colitis in the disease network. This chapter proposes a monitoring programme for assessing wastewater health using a combination of culture independent and culture-dependent molecular techniques in order to prevent the spread of pollutants in tropical environments.

Culture-Independent Exploration of the Hypersaline Ecosystem Indicates the Environment-Specific Microbiome Evolution

Sambhar Salt Lake, situated in the state of Rajasthan, India is a unique temperate hypersaline ecosystem. Exploration of the salt lake microbiome will enable us to understand microbiome functioning in nutrient-deprived extreme conditions, as well as enrich our understanding of the environment-specific microbiome evolution. The current study has been designed to explore the Sambhar Salt Lake microbiome with a culture-independent multi-omics approach to define its metagenomic features and prevalent metabolic functionaries. The rRNA feature and protein feature-based phylogenetic reconstruction synchronously (R = 0.908) indicated the dominance of the archaea (Euryarchaeota) and bacteria (Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria). Metabolic reconstruction identified selective enrichment of the protein features associated with energy harvesting and stress tolerance (osmotic, oxidative, metal/metalloid, heat/cold, antibiotic, and desiccation). Metabolites identified with metabolome analysis confirmed physiological adaptation of the lake microbiome within a hypersaline and nutrient-deprived environment. Comparative metagenomics of the 212 metagenomes representing freshwater, alkaline, and saline ecosystem microbiome indicated the selective enrichment of the microbial groups and genetic features. The current study elucidates microbiome functioning within the nutrient-deprived harsh ecosystems. In summary, the current study harnessing the strength of multi-omics and comparative metagenomics indicates the environment-specific microbiome evolution.

Comparative Metagenomics Reveals Microbial Communities and Their Associated Functions in Two Types of Fuzhuan Brick Tea

Fuzhuan brick tea (FBT) is a unique post-fermented tea product, naturally co-fermented by microorganisms, and has gained global popularity due to its potential health benefits for humans. Considerable efforts have been made toward elucidating the microbial diversity within FBT, but an understanding of the underlying FBT community interactions and functions remains poorly studied. Consequently, the microbial communities of two types of FBT, originating from Hunan and Shaanxi provinces, were investigated using comparative shotgun metagenomic sequencing and functional annotations. Metagenomic analysis indicated that two communities shared similar taxonomic and functional attributes. Two samples shared 486 genera, in which Pseudomonas contributed most to the abundant functions within the two samples. The carbohydrate active enzyme functions of the communities primarily comprised GH (32.92%), GT (26.8%), CEs (20.43%), and AAs (18.04%). Furthermore, the overall metabolic pathways encoded by the metagenomes were largely associated with carbohydrate and amino acid metabolism, with nine metabolic pathways that were differential between two groups including penicillin and cephalosporin biosynthesis. Significantly, a total of 35 potential probiotics were inferred, with Pseudomonas putida being the most abundant inferred probiotic (80%) within the FBT communities. This study provides new insights into FBT microbial communities on their potential functions and roles in FBT characteristics.

Microbiome-Gut-Brain-Axis Communication Influences Metabolic Switch in the Mosquito Anopheles Culicifacies

Periodic ingestion of a protein-rich blood meal by adult female mosquitoes causes a drastic metabolic change in their innate physiological status, which is referred to as ‘metabolic switch. Although the down-regulation of olfactory factors is key to restrain host-attraction, how the gut ‘metabolic switch’ modulates brain functions, and resilience physiological homeostasis remains unexplored. Here we demonstrate that the protein-rich diet induces the expression of brain transcripts related to mitochondrial function and energy metabolism, possibly to cause a shift of the brain’s engagement to manage organismal homeostasis. A dynamic expression pattern of neuro-signalling and neuro-modulatory genes in both gut and brain, establishes an active brain-distant organ communication. Disruption of this comunication through decapitation, does not affect the modulation of the neuro-modulator receptor genes in the gut. In parallel, an unusual and paramount shift in the level of the Neurotransmitters (NTs), from the brain to the gut after blood feeding, further supports the idea of the gut’s ability to serve as a ‘second brain’. Finally, a comparative metagenomics evaluation of gut microbiome population dynamics, highlighted that blood-feeding not only suppresses Enterobacteriaceae family member by 50%, but favors rapid proliferation of Pseudomonadales to 46% of the total community. Notable obesrvation of a rapid proliferation of Pseudomonas bacterial sp. in the gut correlates a possible cause for the suppression of appetite after blood-feeding. Additionally, an altered NTs dynamics of naïve and aseptic mosquitoes provide the initial evidence that gut-endosymbionts are key modulators for the synthesis of major neuroactive molecules. Conclusion: Our data establish a new conceptual understanding of microbiome-gut-brain-axis communication in mosquitoes.Data deposition: Mosquito Brain RNAseq data are accessible under Accession IDs: SRR9853884 (Ac-Br-SF); SRR9853885 (Ac-Br-BF-30Min), SRR9853883 (Ac-Br-BF-30hrs) at NCBI repository. Mosquito Gut metagenomics data are accessible under accession IDs: SRR12579422 (Ac-MG-SF); SRR12622557 (Ac-MG-BF) at NCBI repository.

Genome and Metagenome of The Phytophagous Gall-Inducing Mite Fragariocoptes Setiger (Eriophyoidea): Are Symbiotic Bacteria Responsible For Gall-Formation?

Eriophyoid mites represent a hyperdiverse, phytophagous lineage with an unclear phylogenetic position. These mites have succeeded in colonizing nearly every seed plant species, and this evolutionary success was in part due to the mites' ability to induce galls in plants. A gall is a unique niche that provides the inducer of this modification with vital resources. The exact mechanism of gall formation is still not understood, even as to whether it is endogenic (mites directly cause galls) or exogenic (symbiotic microorganisms are involved). Here we (i) investigate the phylogenetic affinities of eriophyoids and (ii) use comparative metagenomics to test the hypothesis that the endosymbionts of eriophyoid mites are involved in gall-formation. Our phylogenomic analysis robustly inferred eriophyoids as closely related to Nematalycidae, a group of deep-soil mites belonging to Endeostigmata. Our comparative metagenomics, fluorescence in situ hybridization, and electron microscopy experiments identified two candidate endosymbiotic bacteria shared across samples, however, it is unlikely that they are gall-inducers (morphotype1: novel Wolbachia, morphotype2: possibly Agrobacterium tumefaciens). We also detected an array of plant pathogens associated with galls that may be vectored by the mites; a mite pathogenic virus (Betabaculovirus) has the potential to be used in the biocontrol of agricultural pests.