Single-cell genomics and transcriptomics can provide reliable context for assembled genome fragments and gene expression activity on the level of individual prokaryotic genomes. These methods are rapidly emerging as an essential complement to cultivation-based, metagenomics, metatranscriptomics, and microbial community-focused research approaches by allowing direct access to information from individual microorganisms, even from deep-branching phylogenetic groups that currently lack cultured representatives. Their integration and binning with environmental ‘omics data already provides unprecedented insights into microbial diversity and metabolic potential, enabling us to provide information on individual organisms and the structure and dynamics of natural microbial populations in complex environments. This review highlights the pitfalls and recent advances in the field of single-cell omics and its importance in microbiological and biotechnological studies.

Key points

• Single-cell omics expands the tree of life through the discovery of novel organisms, genes, and metabolic pathways.

• Disadvantages of metagenome-assembled genomes are overcome by single-cell omics.

• Functional analysis of single cells explores the heterogeneity of gene expression.

• Technical challenges still limit this field, thus prompting new method developments.

This chapter focuses on how metagenomic data are applied to examine the genomic heterogeneity of natural microbial populations. It highlights the opportunities and challenges inherent to the approach and describes recently developed methods to maximally leverage the potential of these datasets while tackling some of the challenges. We describe how performing population genomic analyses using metagenomic data allows (1) resolution of ecologically and genetically cohesive populations in the environment, (2) tracking of evolutionary processes within them, and (3) application of metatranscriptomic and metaproteomic analyses to determine the in situ physiology of distinct populations. While challenges remain that are inherent to the approach, the current wave of new bioinformatic tools is starting to realize the theoretical potential of metagenomics to peer into the spatiotemporal dynamics of the genetic structure of natural populations.

Since the first two complete bacterial genome sequences were published in 1995, the science of bacteria has dramatically changed. Using third-generation DNA sequencing, it is possible to completely sequence a bacterial genome in a few hours and identify some types of methylation sites along the genome as well. Sequencing of bacterial genome sequences is now a standard procedure, and the information from tens of thousands of bacterial genomes has had a major impact on our views of the bacterial world. In this review, we explore a series of questions to highlight some insights that comparative genomics has produced. To date, there are genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. However, the distribution is quite skewed towards a few phyla that contain model organisms. But the breadth is continuing to improve, with projects dedicated to filling in less characterized taxonomic groups. The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system provides bacteria with immunity against viruses, which outnumber bacteria by tenfold. How fast can we go? Second-generation sequencing has produced a large number of draft genomes (close to 90 % of bacterial genomes in GenBank are currently not complete); third-generation sequencing can potentially produce a finished genome in a few hours, and at the same time provide methlylation sites along the entire chromosome. The diversity of bacterial communities is extensive as is evident from the genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. Genome sequencing can help in classifying an organism, and in the case where multiple genomes of the same species are available, it is possible to calculate the pan- and core genomes; comparison of more than 2000 Escherichia coli genomes finds an E. coli core genome of about 3100 gene families and a total of about 89,000 different gene families. Why do we care about bacterial genome sequencing? There are many practical applications, such as genome-scale metabolic modeling, biosurveillance, bioforensics, and infectious disease epidemiology. In the near future, high-throughput sequencing of patient metagenomic samples could revolutionize medicine in terms of speed and accuracy of finding pathogens and knowing how to treat them.

The endophytic bacteria are universal occupants of the host plant tissues, and microbial endophytic population play an important and distinctive role in the agro-ecosystems functioning. Exploration of the vast diversity of plant-associated and endophytic microbiome has been largely accelerated by the introduction of high-throughput sequencing technologies. Microbial DNA direct amplification from samples of plant tissue and implementation of the massive parallel sequencing technology generates remarkably extensive data that provides an expansive insight into the composition of the plant-associated microbial communities. This review presents an overview of the research experience built up during the decade of application of the next-generation sequencing (NGS) in the metagenomic analysis of the endophytic bacterial communities. We outline the methods and sequencing approaches used in the metagenomic analysis of the plant-associated microbiome and discuss methodological challenges associated with the application of the high-throughput sequencing technology. The metagenomic studies have provided new knowledge about plant genotype- and tissue-specific complexity of the indigenous endophytic communities as well as their dynamics during plant development. Of particular interest are the new insights into the effect of agricultural practices and environmental factors on the endophytic microbiome composition that pave the way to practical implications and development of efficient and sustainable agriculture.

Background and aims

Microbial communities are the primary drivers of organic matter decomposition in peatlands. However, limited knowledge is available regarding depth-dependent microbial community structure and function in East Asian peatlands, using cultivation independent approaches.

Methods

We investigated the vertical stratification of prokaryote and fungal communities in a moderately rich fen in northeast China (Hani) and a rich fen in southwest China (Riganqiao).

Results

Fungal and prokaryotic operational taxonomic unit (OTU) composition exhibited strong site and/or depth responses. Prokaryotic OTUs exhibited the greatest alpha diversity at the mesotelm ‘hot spot’, whereas the predicted metagenomic metabolic functions did not align with the pattern of prokaryote alpha diversity. The large cover of shrubs contributed to a greater relative abundance of ericoid- and ecto-mycorrhizal fungi at Hani, whereas Riganqiao showed more arbuscular mycorrhizal fungi. Soil pH and water table depth were among the predominant abiotic factors associated with microbial community composition.

Conclusions

Projected shifts in hydrology and/or vegetation with global change may cause substantial impacts on peatland microorganisms and thus the associated biogeochemistry. It is critical to better understand the mechanism of the discrepancy between microbial community structure and the functions at the mesotelm ‘hot spot’ when evaluating the ecosystem functions in peatlands.

The bacterial tree of life has recently undergone significant expansion, chiefly from candidate phyla retrieved through genome-resolved metagenomics. Bypassing the need for genome availability, we present a snapshot of bacterial phylogenetic diversity based on the recovery of high-quality SSU rRNA gene sequences extracted from nearly 7000 metagenomes and all available reference genomes. We illuminate taxonomic richness within established bacterial phyla together with environmental distribution patterns, providing a revised framework for future phylogeny-driven sequencing efforts.

Background

Genomes of Methanosarcina spp. are among the largest archaeal genomes. One suggested reason for that is massive horizontal gene transfer (HGT) from bacteria. Genes of bacterial origin may be involved in the central metabolism and solute transport, in particular sugar synthesis, sulfur metabolism, phosphate metabolism, DNA repair, transport of small molecules etc. Horizontally transferred (HT) genes are considered to play the key role in the ability of Methanosarcina spp. to inhabit diverse environments. At the moment, genomes of three Methanosarcina spp. have been sequenced, and while these genomes vary in length and number of protein-coding genes, they all have been shown to accumulate HT genes. However, previous estimates had been made when fewer archaeal genomes were known. Moreover, several Methanosarcinaceae genomes from other genera have been sequenced recently. Here, we revise the census of genes of bacterial origin in Methanosarcinaceae.

Results

About 5 % of Methanosarcina genes have been shown to be horizontally transferred from various bacterial groups to the last common ancestor either of Methanosarcinaceae, or Methanosarcina, or later in the evolution. Simulation of the composition of the NCBI protein non-redundant database for different years demonstrates that the estimates of the HGT rate have decreased drastically since 2002, the year of publication of the first Methanosarcina genome.

The phylogenetic distribution of HT gene donors is non-uniform. Most HT genes were transferred from Firmicutes and Proteobacteria, while no HGT events from Actinobacteria to the common ancestor of Methanosarcinaceae were found. About 50 % of HT genes are involved in metabolism. Horizontal transfer of transcription factors is not common, while 46 % of horizontally transferred genes have demonstrated differential expression in a variety of conditions. HGT of complete operons is relatively infrequent and half of HT genes do not belong to operons.

Conclusions

While genes of bacterial origin are still more frequent in Methanosarcinaceae than in other Archaea, most HGT events described earlier as Methanosarcina-specific seem to have occurred before the divergence of Methanosarcinaceae. Genes horizontally transferred from bacteria to archaea neither tend to be transferred with their regulators, nor in long operons.

Microbial taxonomy should provide adequate descriptions of bacterial, archaeal, and eukaryotic microbial diversity in ecological, clinical, and industrial environments. Its cornerstone, the prokaryote species has been re-evaluated twice. It is time to revisit polyphasic taxonomy, its principles, and its practice, including its underlying pragmatic species concept. Ultimately, we will be able to realize an old dream of our predecessor taxonomists and build a genomic-based microbial taxonomy, using standardized and automated curation of high-quality complete genome sequences as the new gold standard.

Within the marine sphere, host-associated microbiomes are receiving growing attention as prolific sources of novel biocatalysts. Given the known biocatalytic potential of poriferan microbial inhabitants, this review focuses on enzymes from the sponge microbiome, with special attention on their relevant properties and the wide range of their potential biotechnological applications within various industries. Cultivable bacterial and filamentous fungal isolates account for the majority of the enzymatic sources. Hydrolases, mainly glycoside hydrolases and carboxylesterases, are the predominant reported group of enzymes, with varying degrees of tolerance to alkaline pH and growing salt concentrations being common. Prospective areas for the application of these microbial enzymes include biorefinery, detergent, food and effluent treatment industries. Finally, alternative strategies to identify novel biocatalysts from the sponge microbiome are addressed, with an emphasis on modern -omics-based approaches that are currently available in the enzyme research arena. By providing this current overview of the field, we hope to not only increase the appetite of researchers to instigate forthcoming studies but also to stress how basic and applied research can pave the way for new biocatalysts from these symbiotic microbial communities in a productive fashion.

Key points

• The sponge microbiome is a burgeoning source of industrial biocatalysts.

• Sponge microbial enzymes have useful habitat-related traits for several industries.

• Strategies are provided for the future discovery of microbial enzymes from sponges.

Bacteria-inducing legume nodules are known as rhizobia and belong to the class Alphaproteobacteria and Betaproteobacteria. They promote the growth and nutrition of their respective legume hosts through atmospheric nitrogen fixation which takes place in the nodules induced in their roots or stems. In addition, rhizobia have other plant growth-promoting mechanisms, mainly solubilization of phosphate and production of indoleacetic acid, ACC deaminase and siderophores. Some of these mechanisms have been reported for strains of rhizobia which are also able to promote the growth of several nonlegumes, such as cereals, oilseeds and vegetables. Less studied are the mechanisms that have the rhizobia to promote the plant health; however, these bacteria are able to exert biocontrol of some phytopathogens and to induce the plant resistance. In this chapter, we revised the available data about the ability of the legume nodule-inducing bacteria for improving the plant growth, health and nutrition of both legumes and nonlegumes. These data showed that rhizobia meet all the requirements of sustainable agriculture to be used as bio-inoculants allowing the total or partial replacement of chemicals used for fertilization or protection of crops.