Quantitative essentiality in a reduced genome: a functional, regulatory and structural fitness map.

Essentiality studies have traditionally focused on coding regions, often overlooking other small genetic regulatory elements. To address this, we combined transposon libraries containing promoter or terminator sequences to obtain a high-resolution essentiality map of a genome-reduced bacterium, at near-single-nucleotide precision when considering non-essential genes. By integrating temporal transposon-sequencing data by k-means unsupervised clustering, we present a novel essentiality assessment approach, providing dynamic and quantitative information on the fitness contribution of different genomic regions.

Extensive data mining uncovers novel diversity among members of the rare biosphere within the Thermoplasmatota.

Background: Rare species, especially of the marine sedimentary biosphere, have long been overlooked owing to the complexity of sediment microbial communities, their sporadic temporal and patchy spatial abundance, and challenges in cultivating environmental microorganisms. In this study, we combined enrichments, targeted metagenomic sequencing, and extensive data mining to uncover uncultivated members of the archaeal rare biosphere in marine sediments.

Results: In protein-amended enrichments, we detected the ecologically and metabolically uncharacterized class Candidatus Penumbrarchaeia within the phylum Thermoplasmatota.

Host-level biodiversity shapes the dynamics and networks within the coral reef microbiome.

Coral reefs face severe threats from human activity, resulting in drastic biodiversity loss. Despite the urgency of safeguarding these ecosystems, we know little about the ecological impacts of losing coral reef host-associated microbial communities (microbiomes). Here, we experimentally studied the microbiomes attached to or released from seven benthic reef hosts belonging to the functional groups of stony corals, soft corals, macroalgae, and sponges while manipulating the coral reef metacommunity to mimic biodiverse or degraded reef habitats.

Antagonism as a foraging strategy in microbial communities.

In natural habitats, nutrient availability limits bacterial growth. We discovered that bacteria can overcome this limitation by acquiring nutrients by lysing neighboring cells through contact-dependent antagonism. Using single-cell live imaging and isotopic markers, we found that during starvation, the type VI secretion system (T6SS) lysed neighboring cells and thus provided nutrients from lysing cells for growth.

Conserved immunomodulation and variation in host association by Xanthomonadales commensals in Arabidopsis root microbiota.

Suppression of chronic Arabidopsis immune responses is a widespread but typically strain-specific trait across the major bacterial lineages of the plant microbiota. We show by phylogenetic analysis and in planta associations with representative strains that immunomodulation is a highly conserved, ancestral trait across Xanthomonadales, and preceded specialization of some of these bacteria as host-adapted pathogens. Rhodanobacter R179 activates immune responses, yet root transcriptomics suggest this commensal evades host immune perception upon prolonged association.

Assessing environmental gradients in relation to dark CO fixation in estuarine wetland microbiomes.

Unlabelled: The rising atmospheric concentration of CO is a major concern to society due to its global warming potential. In soils, CO-fixing microorganisms are preventing some of the CO from entering the atmosphere. Yet, the controls of dark CO fixation are rarely studied .

High diversity of crustose coralline algae microbiomes across species and islands, and implications for coral recruits.

Background: Crustose Coralline Algae (CCA) play a crucial role in coral reef ecosystems, contributing significantly to reef formation and serving as substrates for coral recruitment. The microbiome associated with CCAs may promote coral recruitment, yet these microbial communities remain largely understudied. This study investigates the microbial communities associated with a large number of different CCA species across six different islands of French Polynesia, and assess their potential influence on the microbiome of coral recruits.

The mOTUs online database provides web-accessible genomic context to taxonomic profiling of microbial communities.

Determining the taxonomic composition (taxonomic profiling) is a fundamental task in studying environmental and host-associated microbial communities. However, genome-resolved microbial diversity on Earth remains undersampled, and accessing the genomic context of taxa detected during taxonomic profiling remains a challenging task. Here, we present the mOTUs online database (mOTUs-db), which is consistent with and interfaces with the mOTUs taxonomic profiling tool.

Metagenomic and -transcriptomic analyses of microbial nitrogen transformation potential, and gene expression in Swiss lake sediments.

The global nitrogen (N) cycle has been strongly altered by anthropogenic activities, including increased input of bioavailable N into aquatic ecosystems. Freshwater sediments are hotspots with regards to the turnover and elimination of fixed N, yet the environmental controls on the microbial pathways involved in benthic N removal are not fully understood. Here, we analyze the abundance and expression of microbial genes involved in N transformations using metagenomics and -transcriptomics across sediments of 12 Swiss lakes that differ in sedimentation rates and trophic regimes.

Trait-based study predicts glycerol/diol dehydratases as a key function of the gut microbiota of hindgut-fermenting carnivores.

Background: Microbial pdu and cob-cbi-hem gene clusters encode the key enzyme glycerol/diol dehydratase (PduCDE), which mediates the transformation of dietary nutrients glycerol and 1,2-propanediol (1,2-PD) to a variety of metabolites, and enzymes for cobalamin synthesis, a co-factor and shared good of microbial communities. It was the aim of this study to relate pdu as a multipurpose functional trait to environmental conditions and microbial community composition. We collected fecal samples from wild animal species living in captivity with different gut physiology and diet (n = 55, in total 104 samples), determined occurrence and diversity of pdu and cob-cbi-hem using a novel approach combining metagenomics with quantification of metabolic and genetic biomarkers, and conducted in vitro fermentations to test for trait-based activity.

In silico RNA isoform screening to identify potential cancer driver exons with therapeutic applications.

Alternative splicing is crucial for cancer progression and can be targeted pharmacologically, yet identifying driver exons genome-wide remains challenging. We propose identifying such exons by associating statistically gene-level cancer dependencies from knockdown viability screens with splicing profiles and gene expression. Our models predict the effects of splicing perturbations on cell proliferation from transcriptomic data, enabling in silico RNA screening and prioritizing targets for splicing-based therapies.

Phenology and ecological role of aerobic anoxygenic phototrophs in freshwaters.

Background: Aerobic anoxygenic phototrophic (AAP) bacteria are heterotrophic bacteria that supply their metabolism with light energy harvested by bacteriochlorophyll-a-containing reaction centers. Despite their substantial contribution to bacterial biomass, microbial food webs, and carbon cycle, their phenology in freshwater lakes remains unknown. Hence, we investigated seasonal variations of AAP abundance and community composition biweekly across 3 years in a temperate, meso-oligotrophic freshwater lake.

The defensome of complex bacterial communities.

Bacteria have developed various defense mechanisms to avoid infection and killing in response to the fast evolution and turnover of viruses and other genetic parasites. Such pan-immune system (defensome) encompasses a growing number of defense lines that include well-studied innate and adaptive systems such as restriction-modification, CRISPR-Cas and abortive infection, but also newly found ones whose mechanisms are still poorly understood. While the abundance and distribution of defense systems is well-known in complete and culturable genomes, there is a void in our understanding of their diversity and richness in complex microbial communities.

A global survey of prokaryotic genomes reveals the eco-evolutionary pressures driving horizontal gene transfer.

Horizontal gene transfer, the exchange of genetic material through means other than reproduction, is a fundamental force in prokaryotic genome evolution. Genomic persistence of horizontally transferred genes has been shown to be influenced by both ecological and evolutionary factors. However, there is limited availability of ecological information about species other than the habitats from which they were isolated, which has prevented a deeper exploration of ecological contributions to horizontal gene transfer.

A cryptic plasmid is among the most numerous genetic elements in the human gut.

Plasmids are extrachromosomal genetic elements that often encode fitness-enhancing features. However, many bacteria carry "cryptic" plasmids that do not confer clear beneficial functions. We identified one such cryptic plasmid, pBI143, which is ubiquitous across industrialized gut microbiomes and is 14 times as numerous as crAssphage, currently established as the most abundant extrachromosomal genetic element in the human gut.

Marine picoplankton metagenomes and MAGs from eleven vertical profiles obtained by the Malaspina Expedition.

The Ocean microbiome has a crucial role in Earth's biogeochemical cycles. During the last decade, global cruises such as Tara Oceans and the Malaspina Expedition have expanded our understanding of the diversity and genetic repertoire of marine microbes. Nevertheless, there are still knowledge gaps regarding their diversity patterns throughout depth gradients ranging from the surface to the deep ocean.

Functional and evolutionary significance of unknown genes from uncultivated taxa.

Many of the Earth's microbes remain uncultured and understudied, limiting our understanding of the functional and evolutionary aspects of their genetic material, which remain largely overlooked in most metagenomic studies. Here we analysed 149,842 environmental genomes from multiple habitats and compiled a curated catalogue of 404,085 functionally and evolutionarily significant novel (FESNov) gene families exclusive to uncultivated prokaryotic taxa. All FESNov families span multiple species, exhibit strong signals of purifying selection and qualify as new orthologous groups, thus nearly tripling the number of bacterial and archaeal gene families described to date.

Metagenome-assembled genomes reveal greatly expanded taxonomic and functional diversification of the abundant marine Roseobacter RCA cluster.

Background: The RCA (Roseobacter clade affiliated) cluster belongs to the family Roseobacteracea and represents a major Roseobacter lineage in temperate to polar oceans. Despite its prevalence and abundance, only a few genomes and one described species, Planktomarina temperata, exist. To gain more insights into our limited understanding of this cluster and its taxonomic and functional diversity and biogeography, we screened metagenomic datasets from the global oceans and reconstructed metagenome-assembled genomes (MAG) affiliated to this cluster.

Ocean-wide comparisons of mesopelagic planktonic community structures.

For decades, marine plankton have been investigated for their capacity to modulate biogeochemical cycles and provide fishery resources. Between the sunlit (epipelagic) layer and the deep dark waters, lies a vast and heterogeneous part of the ocean: the mesopelagic zone. How plankton composition is shaped by environment has been well-explored in the epipelagic but much less in the mesopelagic ocean.