Draft Genome Sequences of a Novel Lineage of Armatimonadetes Recovered from Japanese Hot Springs

Insights into ecological roles of uncultivated bacteria in Katase hot spring sediment from long-read metagenomics

Diverse yet-uncultivated bacteria and archaea, i.e., microbial dark matter, are present in terrestrial hot spring environments. Numerous metagenome-assembled genomes (MAGs) of these uncultivated prokaryotes by short-read metagenomics have been reported so far, suggesting their metabolic potential. However, more reliable MAGs, i.e., circularized complete MAGs (cMAGs), have been rarely reported from hot spring environments. Here, we report 61 high-quality (HQ)-MAGs, including 14 cMAGs, of diverse uncultivated bacteria and archaea retrieved from hot spring sediment (52°C, pH 7.2) by highly accurate long-read sequencing using PacBio Sequel II. The HQ MAGs were affiliated with one archaeal and 13 bacterial phyla. Notably, nine of the 14 cMAGs were the first reported cMAGs for the family- to class-level clades that these cMAGs belonged to. The genome information suggests that the bacteria represented by MAGs play a significant role in the biogeochemical cycling of carbon, nitrogen, iron, and sulfur at this site. In particular, the genome analysis of six HQ MAGs including two cMAGs of Armatimonadota, of which members are frequently abundant in hot spring environments, predicts that they are aerobic, moderate thermophilic chemoorganoheterotrophs, and potentially oxidize and/or reduce iron. This prediction is consistent with the environmental conditions where they were detected. Our results expand the knowledge regarding the ecological potential of uncultivated bacteria in moderately-high-temperature environments.

Complex History of Aerobic Respiration and Phototrophy in the Chloroflexota Class Anaerolineae Revealed by High-Quality Draft Genome of Ca. Roseilinea mizusawaensis AA3_104

Roseilinea is a novel lineage of Chloroflexota known only from incomplete metagenome-assembled genomes (MAGs) and preliminary enrichments. Roseilinea is notable for appearing capable of anoxygenic photoheterotrophy despite being only distantly related to well-known phototrophs in the Chloroflexia class such as Chloroflexus and Roseiflexus. Here, we present a high-quality MAG of a member of Roseilinea, improving our understanding of the metabolic capacity and phylogeny of this genus, and resolving the multiple instances of horizontal gene transfer that have led to its metabolic potential. These data allow us to propose a candidate family for these organisms, Roseilineaceae, within the Anaerolineae class.

Candidatus Anthektikosiphon siderophilum OHK22, a New Member of the Chloroflexi Family Herpetosiphonaceae from Oku-okuhachikurou Onsen

We report the draft metagenome-assembled genome of a member of the Chloroflexi family Herpetosiphonaceae from microbial biofilms developed in a circumneutral, iron-rich hot spring in Japan. This taxon represents a novel genus and species—here proposed as Candidatus Anthektikosiphon siderophilum—that expands the known taxonomic and genetic diversity of the Herpetosiphonaceae and helps orient the evolutionary history of key traits like photosynthesis and aerobic respiration in the Chloroflexi.

Geochemical and Metagenomic Characterization of Jinata Onsen, a Proterozoic-Analog Hot Spring, Reveals Novel Microbial Diversity including Iron-Tolerant Phototrophs and Thermophilic Lithotrophs

Hydrothermal systems, including terrestrial hot springs, contain diverse geochemical conditions that vary over short spatial scales due to progressive interactions between reducing hydrothermal fluids, the oxygenated atmosphere, and, in some cases, seawater. At Jinata Onsen on Shikinejima Island, Japan, an intertidal, anoxic, iron-rich hot spring mixes with the oxygenated atmosphere and seawater over short spatial scales, creating diverse chemical potentials and redox pairs over a distance of ~10 m. We characterized geochemical conditions along the outflow of Jinata Onsen as well as the microbial communities present in biofilms, mats, and mineral crusts along its traverse using 16S rRNA gene amplicon and genome-resolved shotgun metagenomic sequencing. Microbial communities significantly changed downstream as temperatures and dissolved iron concentrations decreased and dissolved oxygen increased. Biomass was more limited near the spring source than downstream, and primary productivity appeared to be fueled by the oxidation of ferrous iron and molecular hydrogen by members of Zetaproteobacteria and Aquificae. The microbial community downstream was dominated by oxygenic Cyanobacteria. Cyanobacteria are abundant and active even at ferrous iron concentrations of ~150 μM, which challenges the idea that iron toxicity limited cyanobacterial expansion in Precambrian oceans. Several novel lineages of Bacteria are also present at Jinata Onsen, including previously uncharacterized members of the phyla Chloroflexi and Calditrichaeota, positioning Jinata Onsen as a valuable site for the future characterization of these clades.

The Landscape of Genetic Content in the Gut and Oral Human Microbiome

Despite substantial interest in the species diversity of the human microbiome and its role in disease, the scale of its genetic diversity, which is fundamental to deciphering human-microbe interactions, has not been quantified. Here, we conducted a cross-study meta-analysis of metagenomes from two human body niches, the mouth and gut, covering 3,655 samples from 13 studies. We found staggering genetic heterogeneity in the dataset, identifying a total of 45,666,334 non-redundant genes (23,961,508 oral and 22,254,436 gut) at the 95% identity level. Fifty percent of all genes were "singletons," or unique to a single metagenomic sample. Singletons were enriched for different functions (compared with non-singletons) and arose from sub-population-specific microbial strains. Overall, these results provide potential bases for the unexplained heterogeneity observed in microbiome-derived human phenotypes. One the basis of these data, we built a resource, which can be accessed at https://microbial-genes.bio.

Evolutionary Implications of Anoxygenic Phototrophy in the Bacterial Phylum Candidatus Eremiobacterota (WPS-2)

Genome-resolved environmental metagenomic sequencing has uncovered substantial previously unrecognized microbial diversity relevant for understanding the ecology and evolution of the biosphere, providing a more nuanced view of the distribution and ecological significance of traits including phototrophy across diverse niches. Recently, the capacity for bacteriochlorophyll-based anoxygenic photosynthesis has been proposed in the uncultured bacterial WPS-2 phylum (recently proposed as Candidatus Eremiobacterota) that are in close association with boreal moss. Here, we use phylogenomic analysis to investigate the diversity and evolution of phototrophic WPS-2. We demonstrate that phototrophic WPS-2 show significant genetic and metabolic divergence from other phototrophic and non-phototrophic lineages. The genomes of these organisms encode a new family of anoxygenic Type II photochemical reaction centers and other phototrophy-related proteins that are both phylogenetically and structurally distinct from those found in previously described phototrophs. We propose the name Candidatus Baltobacterales for the order-level aerobic WPS-2 clade which contains phototrophic lineages, from the Greek for "bog" or "swamp," in reference to the typical habitat of phototrophic members of this clade.

Draft Genome Sequences of Two Basal Members of the Anaerolineae Class of Chloroflexi from a Sulfidic Hot Spring

Here, we describe the first genome sequences of the Anaerolineae from a sulfidic environment, expanding the environmental distribution of sequenced Anaerolineae. These genomes represent basal Anaerolineae lineages, branching soon after the divergence of the sister class “Candidatus Thermofonsia,” expanding our understanding of the metabolic evolution of this group.

Here, we describe the first genome sequences of the Anaerolineae from a sulfidic environment, expanding the environmental distribution of sequenced Anaerolineae. These genomes represent basal Anaerolineae lineages, branching soon after the divergence of the sister class “Candidatus Thermofonsia,” expanding our understanding of the metabolic evolution of this group.

Draft Genome Sequence of a Divergent Anaerobic Member of the Chloroflexi Class Ardenticatenia from a Sulfidic Hot Spring

Here, we present a draft genome sequence of Nak82, the second genome sequence available for the Chloroflexi class Ardenticatenia and the first from a sulfidic terrestrial hot spring. Nak82 is genetically and metabolically distinct from Ardenticatena maritima and likely represents a new genus- or family-level lineage lacking high-potential respiratory pathways.

Here, we present a draft genome sequence of Nak82, the second genome sequence available for the Chloroflexi class Ardenticatenia and the first from a sulfidic terrestrial hot spring. Nak82 is genetically and metabolically distinct from Ardenticatena maritima and likely represents a new genus- or family-level lineage lacking high-potential respiratory pathways.

Evolution of Phototrophy in the Chloroflexi Phylum Driven by Horizontal Gene Transfer

The evolutionary mechanisms behind the extant distribution of photosynthesis is a point of substantial contention. Hypotheses range from the presence of phototrophy in the last universal common ancestor and massive gene loss in most lineages, to a later origin in Cyanobacteria followed by extensive horizontal gene transfer into the extant phototrophic clades, with intermediate scenarios that incorporate aspects of both end-members. Here, we report draft genomes of 11 Chloroflexi: the phototrophic Chloroflexia isolate Kouleothrix aurantiaca as well as 10 genome bins recovered from metagenomic sequencing of microbial mats found in Japanese hot springs. Two of these metagenome bins encode photrophic reaction centers and several of these bins form a metabolically diverse, monophyletic clade sister to the Anaerolineae class that we term Candidatus Thermofonsia. Comparisons of organismal (based on conserved ribosomal) and phototrophy (reaction center and bacteriochlorophyll synthesis) protein phylogenies throughout the Chloroflexi demonstrate that two new lineages acquired phototrophy independently via horizontal gene transfer (HGT) from different ancestral donors within the classically phototrophic Chloroflexia class. These results illustrate a complex history of phototrophy within this group, with metabolic innovation tied to HGT. These observations do not support simple hypotheses for the evolution of photosynthesis that require massive character loss from many clades; rather, HGT appears to be the defining mechanic for the distribution of phototrophy in many of the extant clades in which it appears.