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Three Gram-stain-positive aerobic bacteria, characterized by branched mycelia with putative sporangia, were isolated from forest soil inside a decayed bamboo stem from a geothermal area in West Java, Indonesia. The strain S3.2.2.5 T grew at 15-37 °C (optimum 30 °C), at pH 5.0-7.0 (optimum 7.0) and in the presence of 0-1% NaCl (optimum 0%). Strain S3.2.2.5 T was able to hydrolyse cellulose, xylan, starch and skim milk. The cell-wall sugars were composed of xylose and mannose, and the peptidoglycan hydrolysates contained d-glutamic acid, glycine, d-alanine, l-alanine, β -alanine and l-ornithine. The major fatty acids (>10%) were anteiso-C 17:0 , iso-C 17:0 , C 16:1 2-OH and iso-C 16:1 . The major polar lipids were phosphatidylinositol, phosphatidylglycerol, diphosphatidylglycerol, unidentified glycolipids and unidentified phospholipids. The major menaquinone was MK-9 (H 2 ). The results of the analysis of the phylogenetic tree based on the 16S rRNA gene indicated that these three isolates belong to the genus Dictyobacter and they were most closely related to the type strain of species Dictyobacter aurantiacus S-27 T (97.41-98.00%). The strain S3.2.2.5 T exhibited a genome size of 9.41 Mbp, which was significantly larger than the known Dictyobacter species. The G+C content was 54.3 mol%. The average nucleotide identity (90.77%) and the digital DNA-DNA hybridization values (42.6%) between strain S3.2.2.5 T and D. aurantiacus S-27 T were below the threshold value for species delineation. Based on the phenotypic, chemotaxonomic and molecular characteristics of strain S3.2.2.5 T , a novel species of the genus Dictyobacter , for which the name Dictyobacter halimunensis sp. nov., is proposed. The type strain is S3.2.2.5 T (= UICC B-128 T = CGMCC 1.61913 T = KCTC 43728 T ).

Early characterizations by morphological identification through light microscopy only revealed the presence of a few microbial lineages and the majority of microbial community at the Chae Son hot spring remains uncharacterized. Therefore, this study aims to examine thermophilic microbial communities at the Chae Son hot spring using next-generation sequencing, including investigating hot spring mineralogy. Results suggest that the Chae Son hot spring (49-75 °C, pH = 6.5-7.0) precipitates digitate structures which comprise mainly silica, and that microbial permineralization is primarily through silicification. Alternating layers of mineralized microbial biofilms and silica were observed in digitate sinter cross-sections, contributing to the build-up of microstromatolites. Molecular results revealed that phylogenetically distinct members of photoautotrophic taxa, Chloroflexota and Cyanobacteriota, dominated spring microbial communities (63.19% relative abundance). Potential primary production processes were mainly through photoautotrophy, with minor lithoautotrophic activities (e.g., sulfur cycling and nitrogen cycling). Moreover, overall microbial community and Cyanobacteriota population alpha diversities significantly decreased with increased temperatures. However, no significant correlation was identified between Chloroflexota population diversity and temperatures. This study provides an update on the microbial community using a high-throughput next-generation sequencing technology, including the mineralogy of the Chae Son hot spring, Northern Thailand., Competing Interests: Declarations. Conflict of interest: The authors declare that they have no conflict of interests., (© 2024. The Author(s), under exclusive licence to Springer Nature Japan KK.)

Blue holes are vertical water-filled openings in carbonate rock that exhibit complex morphology, ecology, and water chemistry. In this study, macroscopic microbial mat structures found in complete anoxic conditions in the Faanu Mudugau Blue Hole (Maldives) were studied by metagenomic methods. Such communities have likely been evolutionary isolated from the surrounding marine environment for more than 10,000 years since the Blue Hole formation during the last Ice Age. A total of 48 high-quality metagenome-assembled genomes (MAGs) were recovered, predominantly composed of the phyla Chloroflexota, Proteobacteria and Desulfobacterota. None of these MAGs have been classified to species level (<95% ANI), suggesting the discovery of several new microbial taxa. In particular, MAGs belonging to novel bacterial genera within the order Dehalococcoidales accounted for 20% of the macroscopic mat community. Genome-resolved metabolic analysis of this dominant microbial fraction revealed a mixotrophic lifestyle based on energy conservation via fermentation, hydrogen metabolism and anaerobic CO 2 fixation through the Wood-Ljungdahl pathway. Interestingly, these bacteria showed a high proportion of ancestral genes in their genomes providing intriguing perspectives on mechanisms driving microbial evolution in this peculiar environment. Overall, our results provide new knowledge for understanding microbial life under extreme conditions in blue hole environments., (© 2024 The Author(s). Environmental Microbiology Reports published by John Wiley & Sons Ltd.)

The archaeal mevalonate pathway is a recently discovered modified version of the eukaryotic mevalonate pathway. This pathway is widely conserved in archaea, except for some archaeal lineages possessing the eukaryotic or other modified mevalonate pathways. Although the pathway seems almost exclusive to the domain Archaea, the whole set of homologous genes of the pathway is found in the metagenome-assembled genome sequence of an uncultivated bacterium, Candidatus Promineifilum breve, of the phylum Chloroflexota. To prove the existence of the archaea-specific pathway in the domain Bacteria, we confirmed the activities of the enzymes specific to the pathway, phosphomevalonate dehydratase and anhydromevalonate phosphate decarboxylase, because only these two enzymes are absent in closely related Chloroflexota bacteria that possess a different type of modified mevalonate pathway. The activity of anhydromevalonate phosphate decarboxylase was evaluated by carotenoid production via the archaeal mevalonate pathway reconstituted in Escherichia coli cells, whereas that of phosphomevalonate dehydratase was confirmed by an in vitro assay using the recombinant enzyme after purification and iron-sulfur cluster reconstruction. Phylogenetic analyses of some mevalonate pathway-related enzymes suggest an evolutionary route for the archaeal mevalonate pathway in Candidatus P. breve, which probably involves horizontal gene transfer events.IMPORTANCEThe recent discovery of various modified mevalonate pathways in microorganisms, such as archaea and Chloroflexota bacteria, has shed light on the complexity of the evolution of metabolic pathways, including those involved in primary metabolism. The fact that the archaeal mevalonate pathway, which is almost exclusive to the domain Archaea, exists in a Chloroflexota bacterium provides valuable insights into the molecular evolution of the mevalonate pathways and associated enzymes. Putative genes probably involved in the archaeal mevalonate pathway have also been found in the metagenome-assembled genomes of Chloroflexota bacteria. Such genes can contribute to metabolic engineering for the bioproduction of valuable isoprenoids because the archaeal mevalonate pathway is known to be an energy-saving metabolic pathway that consumes less ATP than other mevalonate pathways do., Competing Interests: The authors declare no conflict of interest.

SAR202 bacteria in the Chloroflexota phylum are abundant and widely distributed in the ocean. Their genome coding capacities indicate their potential roles in degrading complex and recalcitrant organic compounds in the ocean. However, our understanding of their genomic diversity, vertical distribution, and depth-related metabolisms is still limited by the number of assembled SAR202 genomes. In this study, we apply deep metagenomic sequencing (180 Gb per sample) to investigate microbial communities collected from six representative depths at the Bermuda Atlantic Time Series (BATS) station. We obtain 173 SAR202 metagenome-assembled genomes (MAGs). Intriguingly, 154 new species and 104 new genera are found based on these 173 SAR202 genomes. We add 12 new subgroups to the current SAR202 lineages. The vertical distribution of 20 SAR202 subgroups shows their niche partitioning in the euphotic, mesopelagic, and bathypelagic oceans, respectively. Deep-ocean SAR202 bacteria contain more genes and exhibit more metabolic potential for degrading complex organic substrates than those from the euphotic zone. With deep metagenomic sequencing, we uncover many new lineages of SAR202 bacteria and their potential functions which greatly deepen our understanding of their diversity, vertical profile, and contribution to the ocean's carbon cycling, especially in the deep ocean., (© 2024. The Author(s).)

Understanding the composition and spatial distribution patterns of microbial communities in plateau peatland soils is crucial for preserving the structural and functional stability of highland wetlands. We collected 50 soil samples from the core conservation area of Zoige peatland along horizontal and vertical distributions to analyze the soil bacterial and fungal diversity by using high-throughput sequencing technology, combined with Mantel tests and multiple regression on matrices (MRM) statistical methods, as well as the spatial distribution characteristics of community structure similarity at a local scale. The results showed that the dominant soil bacterial and fungal groups were Chloroflexi (accounting for 33.2% and 25.1% of the total bacterial community in horizontal and vertical directions, respectively) and Ascomycota (54.7% and 76.4%). The similarity of microbial community structure in both horizontal and vertical directions decreased with increasing spatial distance of the sampling points. The turnover rates of bacterial and fungal communities in the vertical direction were 8.8 and 8.6 times as those in the horizontal direction, respectively. Based on the relative abundance of the communities, we classified microbes into six groups. As the number of rare species in the community increased, the slope of community distance decay decreased. The conditionally rare or abundant taxa (CRAT) category group showed the most similar spatial distribution characteristics to the total microbial community. Mantel analysis indicated that soil organic carbon, total nitrogen, and available phosphorus were key factors driving the distribution of bacterial and fungal communities in the horizontal direction, while soil organic carbon, available carbon, pH, and soil bulk density were the main factors determining the vertical distribution. MRM analysis further showed that both soil physicochemical indicators and spatial distance significantly affected the assembly of microbial communities, where soil factors explained more about the vertical distribution of microbial communities than the horizontal distribution. The impact of soil factors on microbial community distribution was much greater than that of spatial factors through diffusion limitation. In summary, the microbial communities in the plateau peatland soils exhibited more pronounced vertical distribution differences and environmental response characteristics.

Denitrification plays a central role in the global nitrogen cycle, reducing and removing nitrogen from marine and terrestrial ecosystems. The flux of nitrogen species through this pathway has a widespread impact, affecting ecological carrying capacity, agriculture, and climate. Nitrite reductase (Nir) and nitric oxide reductase (NOR) are the two central enzymes in this pathway. Here we present a previously unreported Nir domain architecture in members of phylum Chloroflexi. Phylogenetic analyses of protein domains within Nir indicate that an ancestral horizontal transfer and fusion event produced this chimeric domain architecture. We also identify an expanded genomic diversity of a rarely reported NOR subtype, eNOR. Together, these results suggest a greater diversity of denitrification enzyme arrangements exist than have been previously reported., (© 2021 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.)

Climate change is altering the frequency and severity of drought events. Recent evidence indicates that drought may produce legacy effects on soil microbial communities. However, it is unclear whether precedent drought events lead to ecological memory formation, i.e., the capacity of past events to influence current ecosystem response trajectories. Here, we utilize a long-term field experiment in a mountain grassland in central Austria with an experimental layout comparing 10 years of recurrent drought events to a single drought event and ambient conditions. We show that recurrent droughts increase the dissimilarity of microbial communities compared to control and single drought events, and enhance soil multifunctionality during drought (calculated via measurements of potential enzymatic activities, soil nutrients, microbial biomass stoichiometry and belowground net primary productivity). Our results indicate that soil microbial community composition changes in concert with its functioning, with consequences for soil processes. The formation of ecological memory in soil under recurrent drought may enhance the resilience of ecosystem functioning against future drought events., (© 2021. The Author(s).)

A mesophilic filamentous anoxygenic phototrophic bacterium, designated M50-1, was isolated from a microbial mat of the Chukhyn Nur soda lake (northeastern Mongolia) with salinity of 5-14 g/L and pH 8.0-9.3. The organism is a strictly anaerobic phototrophic bacterium, which required sulfide for phototrophic growth. The cells formed short undulate trichomes surrounded by a thin sheath and containing gas vesicles. Motility of the trichomes was not observed. The cells contained chlorosomes. The antenna pigments were bacteriochlorophyll d and β- and γ-carotenes. Analysis of the genome assembled from the metagenome of the enrichment culture revealed all the enzymes of the 3-hydroxypropionate bi-cycle for autotrophic CO2 assimilation. The genome also contained the genes encoding a type IV sulfide:quinone oxidoreductase (sqrX). The organism had no nifHDBK genes, encoding the proteins of the nitrogenase complex responsible for dinitrogen fixation. The DNA G + C content was 58.6%. The values for in silico DNA‒DNA hybridization and average nucleotide identity between M50-1 and a closely related bacterium 'Ca. Chloroploca asiatica' B7-9 containing bacteriochlorophyll c were 53.4% and 94.0%, respectively, which corresponds to interspecies differences. Classification of the filamentous anoxygenic phototrophic bacterium M50-1 as a new 'Ca. Chloroploca' species was proposed, with the species name 'Candidatus Chloroploca mongolica' sp. nov., (© The Author(s) 2021. Published by Oxford University Press on behalf of FEMS. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

The aerobic, Gram-positive, mesophilic Ktedonobacteria strains, Uno17 T , SOSP1-1 T , 1-9 T , 1-30 T and 150040 T , formed mycelia of irregularly branched filaments, produced spores or sporangia, and numerous secondary metabolite biosynthetic gene clusters. The five strains grew at 15-40 °C (optimally at 30 °C) and pH 4.0-8.0 (optimally at pH 6.0-7.0), and had 7.21-12.67 Mb genomes with 49.7-53.7 mol% G+C content. They shared MK9(H 2 ) as the major menaquinone and C 16 : 1 -2OH and iso-C 17 : 0 as the major cellular fatty acids. Phylogenetic and phylogenomic analyses showed that Uno17 T and SOSP1-9 T were most closely related to members of the genus Dictyobacter , with 94.43-96.21 % 16S rRNA gene similarities and 72.16-81.56% genomic average nucleotide identity. The strain most closely related to SOSP1-1 T and SOSP1-30 T was Ktedonobacter racemifer SOSP1-21 T , with 91.33 and 98.84 % 16S rRNA similarities, and 75.13 and 92.35% average nucleotide identities, respectively. Strain 150040 T formed a distinct clade within the order Ktedonobacterales , showing <90.47 % 16S rRNA gene similarity to known species in this order. Based on these results, we propose: strain 150040 T as Reticulibacter mediterranei gen. nov., sp. nov. (type strain 150 040 T =CGMCC 1.17052 T =BCRC 81202 T ) within the family Reticulibacteraceae fam. nov. in the order Ktedonobacterales ; strain SOSP1-1 T as Ktedonospora formicarum gen. nov., sp. nov. (type strain SOSP1-1 T =CGMCC 1.17205 T =BCRC 81203 T ) and strain SOSP1-30 T as Ktedonobacter robiniae sp. nov. (type strain SOSP1-30 T =CGMCC 1.17733 T =BCRC 81205 T ) within the family Ktedonobacteraceae ; strain Uno17 T as Dictyobacter arantiisoli sp. nov. (type strain Uno17 T =NBRC 113155 T =BCRC 81116 T ); and strain SOSP1-9 T as Dictyobacter formicarum sp. nov. (type strain SOSP1-9 T =CGMCC 1.17206 T =BCRC 81204 T ) within the family Dictyobacteraceae .

Traditionally, filamentous fungi and actinomycetes are well-known cellulolytic microorganisms that have been utilized in the commercial production of cellulase enzyme cocktails for industrial-scale degradation of plant biomass. Noticeably, the Ktedonobacteria lineage (phylum Chloroflexi) with actinomycetes-like morphology was identified and exhibited diverse carbohydrate utilization or degradation abilities. In this study, we performed genome-wide profiling of carbohydrate-active enzymes (CAZymes) in the filamentous Ktedonobacteria lineage. Numerous CAZymes (153-290 CAZymes, representing 63-131 glycoside hydrolases (GHs) per genome), including complex mixtures of endo- and exo-cellulases, were predicted in 15 available Ktedonobacteria genomes. Of note, 4-28 CAZymes were predicted to be extracellular enzymes, whereas 3-29 CAZymes were appended with carbohydrate-binding modules (CBMs) that may promote their binding to insoluble carbohydrate substrates. This number far exceeded other Chloroflexi lineages and were comparable to the cellulolytic actinomycetes. Six multi-modular extracellular GHs were cloned from the thermophilic Thermosporothrix hazakensis SK20-1 T strain and heterologously expressed. The putative endo-glucanases of ThazG5-1, ThazG9, and ThazG12 exhibited strong cellulolytic activity, whereas the putative exo-glucanases ThazG6 and ThazG48 formed weak but observable halos on carboxymethyl cellulose plates, indicating their potential biotechnological application. The purified recombinant ThazG12 had near-neutral pH (optimal 6.0), high thermostability (60°C), and broad specificity against soluble and insoluble polysaccharide substrates. It also represented described a novel thermostable bacterial β-1,4-glucanase in the GH12 family. Together, this research revealed the underestimated cellulolytic potential of the Ktedonobacteria lineage and highlighted its potential biotechnological utility as a promising microbial resource for the discovery of industrially useful cellulases., (Copyright © 2021 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.)

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.

While microbial communities in the human body (microbiota) are now commonly associated with health and disease in industrialised populations, we know very little about how these communities co-evolved and changed with humans throughout history and deep prehistory. We can now examine these communities by sequencing ancient DNA preserved within calcified dental plaque (calculus), providing insights into the origins of disease and their links to human history. Here, we examine ancient DNA preserved within dental calculus samples and their associations with two major cultural periods in Japan: the Jomon period hunter-gatherers approximately 3000 years before present (BP) and the Edo period agriculturalists 400-150 BP. We investigate how human oral microbiomes have changed in Japan through time and explore the presence of microorganisms associated with oral diseases (e.g. periodontal disease, dental caries) in ancient Japanese populations. Finally, we explore oral microbial strain diversity and its potential links to ancient demography in ancient Japan by performing phylogenomic analysis of a widely conserved oral species- Anaerolineaceae oral taxon 439. This research represents, to our knowledge, the first study of ancient oral microbiomes from Japan and demonstrates that the analysis of ancient dental calculus can provide key information about the origin of non-infectious disease and its deep roots with human demography. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'.

Chloroflexales bacteria are mostly known as filamentous anoxygenic phototrophs that thrive as members of the microbial communities of hot spring cyanobacterial mats. Recently, we described many new Chloroflexales species from non-thermal environments and showed that mesophilic Chloroflexales are more diverse than previously expected. Most of these species were isolated from aquatic environments of mid-latitudes. Here, we present the comprehensive characterization of a new filamentous multicellular anoxygenic phototrophic Chloroflexales bacterium from an Arctic coastal environment (Kandalaksha Gulf, the White Sea). Phylogenomic analysis and 16S rRNA phylogeny indicated that this bacterium belongs to the Oscillochloridaceae family as a new species. We propose that this species be named 'Candidatus Oscillochloris kuznetsovii'. The genomes of this species possessed genes encoding sulfide:quinone reductase, the nitrogenase complex and the Calvin cycle, which indicate potential for photoautotrophic metabolism. We observed only mesophilic anaerobic anoxygenic phototrophic growth of this novel bacterium. Electron microphotography showed the presence of chlorosomes, polyhydroxyalkanoate-like granules and polyphosphate-like granules in the cells. High-performance liquid chromatography also revealed the presence of bacteriochlorophylls a, c and d as well as carotenoids. In addition, we found that this bacterium is present in benthic microbial communities of various coastal environments of the Kandalaksha Gulf., (© The Author(s) 2020. Published by Oxford University Press on behalf of FEMS.)

Photosynthetic bacteria are abundant in alkaline, terrestrial hot springs and there is a long history of research on phototrophs in Yellowstone National Park (YNP). Hot springs provide a framework to examine the ecophysiology of phototrophs in situ because they provide natural gradients of geochemistry, pH and temperature. Phototrophs within the Cyanobacteria and Chloroflexi groups are frequently observed in alkaline hot springs. Decades of research has determined that temperature constrains Cyanobacteria in alkaline hot springs, but factors that constrain the distribution of phototrophic Chloroflexi remain unresolved. Using a combination of 16S rRNA gene sequencing and photoassimilation microcosms, we tested the hypothesis that temperature would constrain the activity and composition of phototrophic Cyanobacteria and Chloroflexi. We expected diversity and rates of photoassimilation to decrease with increasing temperature. We report 16S rRNA amplicon sequencing along with carbon isotope signatures and photoassimilation from 45 to 72°C in two alkaline hot springs. We find that Roseiflexus, Chloroflexus (Chloroflexi) and Leptococcus (Cyanobacteria) operational taxonomic units (OTUs) have distinct distributions with temperature. This distribution suggests that, like phototrophic Cyanobacteria, temperature selects for specific phototrophic Chloroflexi taxa. The richness of phototrophic Cyanobacteria decreased with increasing temperature along with a decrease in oxygenic photosynthesis, whereas Chloroflexi richness and rates of anoxygenic photosynthesis did not decrease with increasing temperature, even at temperatures approaching the upper limit of photosynthesis (~72-73°C). Our carbon isotopic data suggest an increasing prevalence of the 3-hydroxypropionate pathway with decreasing temperature coincident with photoautotrophic Chloroflexi. Together these results indicate temperature plays a role in defining the niche space of phototrophic Chloroflexi (as has been observed for Cyanobacteria), but other factors such as morphology, geochemistry, or metabolic diversity of Chloroflexi, in addition to temperature, could determine the niche space of this highly versatile group., (© 2020 The Authors. Environmental Microbiology Reports published by Society for Applied Microbiology and John Wiley & Sons Ltd.)

The soil organic carbon (SOC) mineralization rate in sandy soil plays an important role in improving soil quality, and a research is needed to determine management practices that optimize the mineralization rate. When sandy soil is improved by adding soft rock, the specific promotion process of bacterium to SOC mineralization remain unclear. To investigate these mechanisms, we selected four treatments with soft rock to sand volume ratios of 0:1 (CK), 1:5 (C1), 1:2 (C2) and 1:1 (C3) to study. The mineralization rate of organic carbon was measured using the lye absorption method. High-throughput sequencing and scanning electron microscopy were used to determine the bacterial community structure and soil microstructure, respectively. The results showed that the organic carbon content of the sandy soil increased significantly (182.22-276.43%) after using the soft rock treatments. The SOC mineralization rate could be divided into two stages: a rapid decline during days 1-8 and a slow decline during days 8-60. With increased incubation time, the intensity of the cumulative release of organic carbon gradually weakened. Compared with the CK treatment, the SOC mineralization accumulation (Ct) and the potential mineralizable organic carbon content (C 0 ) in the C1, C2, and C3 treatments increased significantly, by 106.98-225.94% and 112.22-254.08%, respectively. The cumulative mineralization rate (Cr) was 18.11% and 21.38% smaller with treatments C2 and C3, respectively. The SOC mineralization rate constant (k) decreased significantly after the addition of soft rock, while the half-turnover period (Th) changed inversely with k. Compared with the CK treatment, the number of gene copies of the soil bacteria increased by 15.38-272.53% after adding soft rock, with the most significant increase in treatment C3. The bacterial diversity index also increased significantly under treatment C3. The three dominant bacteria were Proteobacteria, Actinobacteria, and Chloroflexi. The correlation between C r and one of the non-dominant bacteria, Firmicutes, was large, and the bacteria had a significant positive correlation with k. At the same time, the abundance of Firmicutes under treatments C2 and C3 was small. As the proportion of soft rock increased, the soil particles changed from point contact to surface contact, and the adhesion on the surface of the particles gradually increased. Results from this study show that the retention time of SOC can be increased and the carbon sequestration effect is better when the ratio of soft rock to sand is set to 1:2.

Recent advances in sequencing technology and bioinformatic pipelines have allowed unprecedented access to the genomes of yet-uncultivated microorganisms from diverse environments. However, the catalogue of freshwater genomes remains limited, and most genome recovery attempts in freshwater ecosystems have only targeted specific taxa. Here, we present a genome recovery pipeline incorporating iterative subtractive binning, and apply it to a time series of 100 metagenomic datasets from seven connected lakes and estuaries along the Chattahoochee River (Southeastern USA). Our set of metagenome-assembled genomes (MAGs) represents >400 yet-unnamed genomospecies, substantially increasing the number of high-quality MAGs from freshwater lakes. We propose names for two novel species: 'Candidatus Elulimicrobium humile' ('Ca. Elulimicrobiota', 'Patescibacteria') and 'Candidatus Aquidulcis frankliniae' ('Chloroflexi'). Collectively, our MAGs represented about half of the total microbial community at any sampling point. To evaluate the prevalence of these genomospecies in the chronoseries, we introduce methodologies to estimate relative abundance and habitat preference that control for uneven genome quality and sample representation. We demonstrate high degrees of habitat-specialization and endemicity for most genomospecies in the Chattahoochee lakes. Wider ecological ranges characterized smaller genomes with higher coding densities, indicating an overall advantage of smaller, more compact genomes for cosmopolitan distributions., (© 2020 Society for Applied Microbiology and John Wiley & Sons Ltd.)

Members of the bacterial candidate phylum WPS-2 (or Eremiobacterota) are abundant in several dry, bare soil environments. In a bare soil deposited by an extinct iron-sulfur spring, we found that WPS-2 comprised up to 24% of the bacterial community and up to 10 8 cells per g of soil based on 16S rRNA gene sequencing and quantification. A single genus-level cluster (Ca. Rubrimentiphilum) predominated in bare soils but was less abundant in adjacent forest. Nearly complete genomes of Ca. Rubrimentiphilum were recovered as single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs). Surprisingly, given the abundance of WPS-2 in bare soils, the genomes did not indicate any capacity for autotrophy, phototrophy, or trace gas metabolism. Instead, they suggest a predominantly aerobic organoheterotrophic lifestyle, perhaps based on scavenging amino acids, nucleotides, and complex oligopeptides, along with lithotrophic capacity on thiosulfate. Network analyses of the entire community showed that some species of Chloroflexi, Actinobacteria, and candidate phylum AD3 (or Dormibacterota) co-occurred with Ca. Rubrimentiphilum and may represent ecological or metabolic partners. We propose that Ca. Rubrimentiphilum act as efficient heterotrophic scavengers. Combined with previous studies, these data suggest that the phylum WPS-2 includes bacteria with diverse metabolic capabilities., (© 2020 Society for Applied Microbiology and John Wiley & Sons Ltd.)

Methylmercury is a neurotoxin that bioaccumulates from seawater to high concentrations in marine fish, putting human and ecosystem health at risk. High methylmercury levels have been found in the oxic subsurface waters of all oceans, but only anaerobic microorganisms have been shown to efficiently produce methylmercury in anoxic environments. The microaerophilic nitrite-oxidizing bacteria Nitrospina have previously been suggested as possible mercury methylating bacteria in Antarctic sea ice. However, the microorganisms responsible for processing inorganic mercury into methylmercury in oxic seawater remain unknown. Here, we show metagenomic and metatranscriptomic evidence that the genetic potential for microbial methylmercury production is widespread in oxic seawater. We find high abundance and expression of the key mercury methylating genes hgcAB across all ocean basins, corresponding to the taxonomic relatives of known mercury methylating bacteria from Deltaproteobacteria, Firmicutes and Chloroflexi. Our results identify Nitrospina as the predominant and widespread microorganism carrying and actively expressing hgcAB. The highest hgcAB abundance and expression occurs in the oxic subsurface waters of the global ocean where the highest MeHg concentrations are typically observed., (© 2020 Society for Applied Microbiology and John Wiley & Sons Ltd.)

An aerobic, Gram-stain-positive, mesophilic Ktedonobacteria strain, W12 T , was isolated from soil of the Mt Zao volcano in Miyagi, Japan. Cells were filamentous, non-motile, and grew at 20-37 °C (optimally at 30 °C), at pH 5.0-7.0 (optimally at pH 6.0) and with <2 % (w/v) NaCl on 10-fold diluted Reasoner's 2A (R2A) medium. Oval-shaped spores were formed on aerial mycelia. Strain W12 T hydrolysed microcrystalline cellulose and xylan very weakly, and used d-glucose as its sole carbon source. The major menaquinone was MK-9, and the major cellular fatty acids were C 16 : 1 2-OH, iso-C 17 : 0 , summed feature 9 (10-methyl C 16 : 0 and/or iso-C 17 : 1 ω9 c ) and anteiso-C 17 : 0 . Cell-wall sugars were mannose and xylose, and cell-wall amino acids were d-glutamic acid, glycine, l-serine, d-alanine, l-alanine, β-alanine and l-ornithine. Polar lipids were phosphatidylinositol, phosphatidylglycerol, diphosphatidylglycerol, an unidentified glycolipid and an unidentified phospholipid. Strain W12 T has a genome of 7.42 Mb with 49.7 mol% G+C content. Nine copies of 16S rRNA genes with a maximum dissimilarity of 1.02 % and 13 biosynthetic gene clusters mainly coding for peptide products were predicted in the genome. Phylogenetic analysis based on both 16S rRNA gene and whole genome sequences indicated that strain W12 T represents a novel species in the genus Dictyobacter . The most closely related Dictyobacter type strain was Dictyobacter alpinus Uno16 T , with 16S rRNA gene sequence similarity and genomic average nucleotide identity of 98.37 % and 80.00 %, respectively. Herein, we propose the name Dictyobacter vulcani sp. nov. for the type strain W12 T (=NBRC 113551 T =BCRC 81169 T ) in the bacterial class Ktedonobacteria .

A novel aerobic moderately thermophilic bacterium, strain 3753O T , was isolated from a Chukotka hot spring (Arctic, Russia) using the newly developed technology of laser engineering of microbial systems. Сells were regular short rods, 0.4×0.8-2.0 µm in size, with a monoderm-type envelope and a single flagellum. The temperature and pH ranges for growth were 42-60 °C and pH 6.5-8.5, the optima being 50-54 °C and pH 7.3. Strain 3753O T grew chemoorganoheterotrophically on a number of carbohydrates or peptidic substrates and volatile fatty acids, and chemolithoautotrophically with siderite (FeCO 3 ) as the electron donor. The major cellular fatty acid was branched C 19 : 0 . Phosphatidylethanolamine, phosphatidylglycerol and two unidentified phospholipids as well as two yellow carotenoid-type pigments were detected in the polar lipid extract. Strain 3753O T was inhibited by chloramphenicol, polymyxin B, vancomycin, streptomycin, neomycin and kanamycin, but resistant to the action of novobiocin and ampicillin. The DNA G+C content was 69.9 mol%. The 16S rRNA gene as well as 51 conservative protein sequence-based phylogenetic analyses placed strain 3753O T within the previously uncultivated lineage OLB14 in the phylum Chloroflexi . Taking into account the phylogenetic position as well as phenotypic properties of the novel isolate, the novel genus and species Tepidiforma bonchosmolovskayae gen. nov. , sp. nov., within the Tepidiformaceae fam. nov., the Tepidiformales ord. nov. and the Tepidiformia classis nov. are proposed. The type strain of Tepidiforma bonchosmolovskayae is 3753O T (=VKM B-3389 T =KTCT 72284 T ).

A novel filamentous, spore-forming, Gram-stain-positive bacterium, designated SCAWS-G2 T , was isolated from red soil in Jiangxi Province, PR China. The strain grew at 25-45 °C and at pH 4.0-7.0, and was able to tolerate up to 50 mM Zn 2+ . The complete genome of strain SCAWS-G2 T was a circular chromosome of ~11.34 Mb, which contained four 16S rRNA genes with three sequence types (0.4-0.8 % differences). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SCAWS-G2 T formed a distinct lineage within the order Ktedonobacterales , showing <89.2 % sequence similarities to the recognized taxa of this order. The whole-genome based phylogenomic tree separated strain SCAWS-G2 T from the recognized families within Ktedonobacterales . The genome-wide average nucleotide identity values between strain SCAWS-G2 T and the related type strains were <68.2 %. The strain can also be differentiated from the recognized families by a number of phenotypic characteristics. The polar lipids of SCAWS-G2 T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, seven unidentified glycolipids and one unidentified lipid. The peptidoglycan amino acids contained ornithine, glycine, glutamic acid and alanine, and the cell-wall sugars were mainly galactose and rhamnose. The major fatty acids were C 16 : 1 2-OH, C 16 : 0 and iso-C 17 : 0 . Based on all these data, we propose that strain SCAWS-G2 T represents a novel genus and species, Ktedonosporobacter rubrisoli gen. nov., sp. nov., within the new family Ktedonosporobacteraceae fam. nov. of the order Ktedonobacterales . The type strain of Ktedonosporobacter rubrisoli is SCAWS-G2 T (=CGMCC 1.16132 T =DSM 105258 T ).

Currently, actinomycetes and myxobacteria are the only bacteria believed to form sporangia. Here, we describe a sporangium-forming process identified in Dictyobacter aurantiacus strain S27 T belonging to the class Ktedonobacteria in the phylum Chloroflexi. Microscopic observations showed that strain S27 T forms a substrate mycelium and subsequently produces globose or subglobose terminal sporangia arising from the vegetative mycelia through short stalk cells. This morphogenetic differentiation is similar to that seen in members of Actinoplanes belonging to the class Actinobacteria. However, unlike in Actinoplanes, motile spores could not be observed. This is the first report of the existence of a bacterium, other than actinomycetes and myxobacteira, with a complex morphogenetic differentiation that forms sporangia and is an important microbiological discovery.

The Laurentian Great Lakes are a vast, interconnected freshwater system spanning strong physicochemical gradients, thus constituting a powerful natural laboratory for addressing fundamental questions about microbial ecology and evolution. We present a comparative analysis of pelagic microbial communities across all five Laurentian Great Lakes, focusing on Bacterial and Archaeal picoplankton characterized via 16S rRNA amplicon sequencing. We collected samples throughout the water column from the major basins of each lake in spring and summer over 2 years. Two oligotypes, classified as LD12 (Alphaproteobacteria) and acI-B1 (Actinobacteria), were among the most abundant in every sample. At the same time, microbial communities showed distinct patterns with depth during summer stratification. Deep hypolimnion samples were frequently dominated by a Chloroflexi oligotype that reached up to 19% relative abundance. Stratified surface communities differed between the colder, less productive upper lakes (Superior, Michigan, Huron) and warmer, more productive lower lakes (Erie, Ontario), in part due to an Actinobacteria oligotype (acI-C2) that averaged 7.7% of sequences in the lower lakes but <0.2% in the upper lakes. Together, our findings suggest that both hydrologic connectivity and local selective pressures shape microbial communities in the Great Lakes and establish a framework for future investigations., (© 2019 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.)

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.

Microorganisms play important roles in soil improvement. Therefore, clarifying the contribution of environmental factors in shaping the microbial community structure is beneficial to improve soil fertility in karst rocky desertification areas. Here, the bacterial community structures of eight rhizospheric soil samples collected from perennial fruit plantations were analysed using an Illumina HiSeq2500 platform. The diversity and abundance of bacteria in rocky desertification areas were significantly lower than those in non-rocky desertification areas, while the bacterial community structure was not significantly different between root surface and non-root surface soils in the same rhizospheric soil samples. Proteobacteria predominated in rocky desertification areas, while Actinobacteria predominated in non-rocky desertification areas. Correlation analysis revealed that water-soluble phosphorus content (r 2  = 0.8258), latitude (r 2  = 0.7556), altitude (r 2  = 0.7501), and the age of fruit trees (r 2  = 0.7321) were positively correlated with the bacterial community structure, while longitude, pH, and total phosphorus content did not significantly influence the soil bacterial community structure. As water-soluble phosphorus content is derived from insoluble phosphorus minerals, supplementing phosphorus-solubilising bacteria to soils in rocky desertification areas is a feasible strategy for accelerating the dissolution of insoluble phosphorus minerals and improving agricultural production and environment ecology.

The low temperature and elevated hydrostatic pressure in hadal trenches at water depths below 6000 m render sample collection difficult. Here, in situ hadal water microbial samples were collected from the Mariana Trench and analysed. The hadal microbial communities at different depths were revealed to be consistent and were dominated by heterotrophic Marinimicrobia. Thirty high-quality metagenome-assembled genomes (MAGs) were retrieved to represent the major hadal microbes affiliated with 12 prokaryotic phyla. Most of the MAGs were newly reported and probably derived from novel hadal inhabitants as exemplified by a potentially new candidate archaeal phylum in the DPANN superphylum. Metabolic reconstruction indicated that a great number of the MAGs participated in nitrogen and sulfur cycling, in which the nitrification process was driven sequentially by Thaumarchaeota and Nitrospirae and sulfur oxidization by Rhodospirillales in the Alphaproteobacteria class. Moreover, several groups of hadal microbes were revealed to be potential carbon monoxide oxidizers. Metatranscriptomic result highlighted the contribution of Chloroflexi in degrading recalcitrant dissolved organic matter and Marinimicrobia in extracellular protein decomposition. The present work provides an in-depth view on the hadal microbial communities regarding their endemism and element cycles., (© 2019 Society for Applied Microbiology and John Wiley & Sons Ltd.)

Control of common scab disease can be reached by resistant cultivars or suppressive soils. Both mechanisms are likely to translate into particular potato microbiome profiles, but the relative importance of each is not known. Here, microbiomes of bulk and tuberosphere soil and of potato periderm were studied in one resistant and one susceptible cultivar grown in a conducive and a suppressive field. Disease severity was suppressed similarly by both means yet, the copy numbers of txtB gene (coding for a pathogenicity determinant) were similar in both soils but higher in periderms of the susceptible cultivar from conducive soil. Illumina sequencing of 16S rRNA genes for bacteria (completed by 16S rRNA microarray approach) and archaea, and of 18S rRNA genes for micro-eukarytes showed that in bacteria, the more important was the effect of cultivar and diversity decreased from resistant cultivar to bulk soil to susceptible cultivar. The major changes occurred in proportions of Actinobacteria, Chloroflexi, and Proteobacteria. In archaea and micro-eukaryotes, differences were primarily due to the suppressive and conducive soil. The effect of soil suppressiveness × cultivar resistance depended on the microbial community considered, but differed also with respect to soil and plant nutrient contents particularly in N, S and Fe.

Natural attenuation of polychlorinated biphenyls (PCBs) by indigenous bacteria is an effective remediation strategy for polluted marine sediments. This study investigated the relationships between PCB concentrations in sediment pore water, humin electron transfer capacity, and potential PCB dechlorinators at eight sediment sampling sites in the southern Yellow Sea, China, with differential PCB contamination. Station A2 showed the highest PCB concentration (453.16 ng L -1 for seven indicator PCBs), especially of less chlorinated PCB congeners (≤5 Cl atoms), humin redox activity, and Dehalococcoides abundance (p < 0.05). Statistical analyses revealed a highly positive correlation between Dehalococcoides abundance and PCB concentration (r = 0.836, p < 0.05) and the electron shuttling ability of humins (r = 0.952, p < 0.01), whereas this was not observed for total bacteria and other potential PCB dechlorinators, e.g., Dehalobacter and Dehalogenimonas. Based on these results, Dehalococcoides might play an important role in the in situ reductive dechlorination of PCBs involving humins in marine sediments, and the natural microbial PCB attenuation capacity at station A2 was high. Chemical characterizations, electrochemical properties, and Fourier transform infrared analysis suggested that humins at station A2 had the highest electron transfer capacity. Furthermore, quinones are likely to be the functional groups that shuttle electrons during PCB dechlorination. Overall, this study provides a useful foundation for evaluating the natural microbial attenuation potential and fates of PCBs in marine sediments and for determining the role of humins as redox mediators in in situ PCB dechlorination by putative indigenous dechlorinators., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Three mesophilic, Gram-stain-positive, aerobic bacterial strains, designated Uno3 T , Uno11 T and Uno16 T , were isolated from a soil-like granular micro-organism mass (termed Tengu-no-mugimeshi) collected from Tsumagoi, Gunma, Japan. They grow at 11-37 °C and pH 4.0-8.0, form branched mycelia, and have a G+C content between 49.4-50.3 mol%. The major menaquinone and fatty acid of Uno3 T are MK-9 and iso-C16 : 0, respectively, whereas Uno11 T and Uno16 T share MK-9 (H2) and C16 : 1-2OH. The major cell-wall sugars are mannose (Uno3 T and Uno11 T ) and glucose (Uno16 T ). Phylogenetic analysis based on 16S rRNA gene sequences indicated that these three strains belong to the order Ktedonobacterales and are most closely related to Dictyobacter aurantiacus S-27 T (sequence similarity of 91.3, 96.4 and 95.5 %). Average nucleotide identity values were <79.9 % among Uno11 T , Uno16 T and D. aurantiacus S-27 T , well below the 95-96 % species circumscription threshold. Based on phenotypic features and phylogenetic positions, we propose that Uno3 T represents a novel genus and species, Tengunoibacter tsumagoiensis gen. nov., sp. nov. (type strain Uno3 T =NBRC 113152 T =LMG 30471 T =BCRC 81113 T ) within the new family Dictyobacteraceae fam. nov. Strains Uno11 T and Uno16 T are also considered to represent novel species: Dictyobacterkobayashii sp. nov. (type strain Uno11 T =NBRC 113153 T =LMG 30472 T =BCRC 81114 T ) and Dictyobacteralpinus sp. nov. (type strain Uno16 T =NBRC 113154 T =BCRC 81115 T ). We also propose an emended description of the genus Dictyobacter, classifying it within family Dictyobacteraceae, and provide emended descriptions of the genera Dictyobacter and Ktedonobacter.

Two thermophilic, aerobic, Gram-stain-positive Ktedonobacteria strains, A1-2 T and A3-2 T , were isolated from geothermal soil in Japan. The strains formed orange-coloured colonies on 10-fold diluted Reasoner's 2A medium, followed by formation of branched aerial mycelium with multiple grape-like spores. Both strains hydrolysed casein, carboxymethyl cellulose, starch, chitin and xylan, but did not liquify gelatin. Strain A1-2 T utilised sucrose and gellan gum and was inhibited by inositol, while strain A3-2 T utilised only gellan gum and was not inhibited by inositol. The DNA G+C contents of strain A1-2 T and A3-2 T were 63.2 and 63.1 mol%, respectively. Chemotaxonomic data (major fatty acid, iso-C17 : 0; major menaquinone, MK-9(H2); cell-wall amino acids, ornithine, serine, glycine, glutamic acid, alanine and β-alanine; polar lipids, phosphatidylinositol, phosphatidylglycerol, diphosphatidylglycerol, one unidentified lipid, one unidentified phosphoglycolipid and three unidentified glycolipids; major cell-wall sugars, mannose, arabinose and xylose) indicate that both strains belong to the genus Thermogemmatispora. 16S rRNA gene sequence analysis indicated that strain A1-2  T was most closely related to the type strains of Thermogemmatispora onikobensis (97.7 % sequence similarity), and that strain A3-2 T was most closely related to the type strains of Thermogemmatispora carboxidivorans(97.2%), but DNA-DNA hybridization shows relatedness values of <67 % with previously described type strains. Moreover, 16S rRNA gene sequence similarity and DNA-DNA relatedness between strain A1-2 T and strain A3-2 T were 96.0 and 33.4%, respectively, suggesting that the two strains are genetically distinct. The two strains are proposed as Thermogemmatispora aurantia sp. nov. and Thermogemmatispora argillosa sp. nov.

Background: Peanut ( Arachis hypogaea L.), an important oilseed and food legume, is widely cultivated in the semi-arid tropics. Drought is the major stress in this region which limits productivity. Microbial communities in the rhizosphere are of special importance to stress tolerance. However, relatively little is known about the relationship between drought and microbial communities in peanuts., Method: In this study, deep sequencing of the V3-V4 region of the 16S rRNA gene was performed to characterize the microbial community structure of drought-treated and untreated peanuts., Results: Taxonomic analysis showed that Actinobacteria, Proteobacteria, Saccharibacteria, Chloroflexi, Acidobacteria and Cyanobacteria were the dominant phyla in the peanut rhizosphere. Comparisons of microbial community structure of peanuts revealed that the relative abundance of Actinobacteria and Acidobacteria dramatically increased in the seedling and podding stages in drought-treated soil, while that of Cyanobacteria and Gemmatimonadetes increased in the flowering stage in drought-treated rhizospheres. Metagenomic profiling indicated that sequences related to metabolism, signaling transduction, defense mechanism and basic vital activity were enriched in the drought-treated rhizosphere, which may have implications for plant survival and drought tolerance., Conclusion: This microbial communities study will form the foundation for future improvement of drought tolerance of peanuts via modification of the soil microbes.

A novel slow-growing, facultatively anaerobic, filamentous bacterium, strain MO-CFX2 T , was isolated from a methanogenic microbial community in a continuous-flow bioreactor that was established from subseafloor sediment collected off the Shimokita Peninsula of Japan. Cells were multicellular filamentous, non-motile and Gram-stain-negative. The filaments were generally more than 20 µm (up to approximately 200 µm) long and 0.5-0.6 µm wide. Cells possessed pili-like structures on the cell surface and a multilayer structure in the cytoplasm. Growth of the strain was observed at 20-37 °C (optimum, 30 °C), pH 5.5-8.0 (pH 6.5-7.0), and 0-30 g l -1 NaCl (5 g l -1 NaCl). Under optimum growth conditions, doubling time and maximum cell density were estimated to be approximately 19 days and ~10 5 cells ml -1 , respectively. Strain MO-CFX2 T grew chemoorganotrophically on a limited range of organic substrates in anaerobic conditions. The major cellular fatty acids were saturated C16 : 0 (47.9 %) and C18 : 0 (36.9 %), and unsaturated C18 : 1ω9c (6.0 %) and C16 : 1ω7 (5.1 %). The G+C content of genomic DNA was 63.2 mol%. 16S rRNA gene-based phylogenetic analysis showed that strain MO-CFX2 T shares a notably low sequence identity with its closest relatives, which were Thermanaerothrix daxensis GNS-1 T and Thermomarinilinea lacunifontana SW7 T (both 85.8 % sequence identity). Based on these phenotypic and genomic properties, we propose the name Aggregatilinea lenta gen. nov., sp. nov. for strain MO-CFX2 T (=KCTC 15625 T , =JCM 32065 T ). In addition, we also propose the associated family and order as Aggregatilineaceae fam. nov. and Aggregatilineales ord. nov., respectively.

We present the results of a study of mesophilic anoxygenic phototrophic Chloroflexota bacteria from Mechigmen hot spring (the Chukotka Peninsula) and Siberia. According to 16S rRNA phylogenetic analysis, these bacteria belong to Oscillochloris trichoides. However, sequencing the draft genome of the bacterium from the Chukotka and analysis of the average nucleotide identity, as well as in silico DNA-DNA hybridization, reveal that this bacterium belongs to a novel species within the Oscillochloris genus. We, therefore, propose 'Candidatus Oscillochloris fontis' as a novel taxon to represent this mesophilic alkaliphilic anaerobic anoxygenic phototrophic bacterium. Spectrophotometry and high-performance liquid chromatography analysis show that the bacterium possesses bacteriochlorophylls c and a, as well as lycopene, β-carotene and γ-carotene. In addition, transmission electron microscopy shows the presence of chlorosomes, polyhydroxyalkanoate- and polyphosphate-like granules. The genome of 'Ca. Oscillochloris fontis' and the Siberian strains of Oscillochloris sp. possess the key genes for nitrogenase complex (nifH) and ribulose-1,5-bisphosphate carboxylase/oxygenase (cbbL), as previously described for O. trichoides DG-6. The results presented here, and previously published data, show that Oscillochloris bacteria from different aquatic environments have the potential for CO2 and N2 fixation. Additionally, we describe a new primer system for the detection of RuBisCo form I., (© FEMS 2019.)

In this article, we present the description of a novel mesophilic phototrophic Chloroflexi bacterium, 'Candidatus Viridilinea mediisalina' Kir15-3F. We have isolated an anaerobic, highly enriched culture of this bacterium from the Kiran soda lake (Siberia) and optimized its cultivation. Metagenomic sequencing revealed that 'Ca. Viridilinea mediisalina' Kir15-3F is a bacteriochlorophyll-containing Chloroflexi bacterium in the enrichment culture. Fluorescent in situ hybridisation demonstrated a link between the phenotype described here and the 'Ca. Viridilinea mediisalina' Kir15-3F genome. Spectrophotometry and high-performance liquid chromatography analyses showed the presence of bacteriochlorophylls d, c and a, as well as lycopene, γ-carotene and β-carotene. Transmission electron microscopy showed chlorosomes, gas vesicles, polyhydroxyalkanoate-like and polyphosphate-like granules. Our results illustrated that 'Ca. Viridilinea mediisalina' Kir15-3F is an alkaliphilic, salt-tolerant, obligately mesophilic, anaerobic, phototrophic bacterium. The genome sequences lack genes of the Calvin cycle and a sulphide:quinone reductase gene for sulphide oxidation. Owing to the lack of an axenic culture and based on the genomic and phenotypic data, we have presented the description of the bacterium in the Candidatus category., (© FEMS 2019.)

Filamentous bacteria belonging to the phylum Chloroflexi have received considerable attention in wastewater treatment systems for their suggested role in the operational problem of impaired sludge settleability known as bulking. Their consistently high abundance in full-scale systems, even in the absence of bulking, indicates that they make a substantial contribution to the nutrient transformations during wastewater treatment. In this study, extensive 16S rRNA amplicon surveys of Danish wastewater treatment plants (WWTPs) with nutrient removal were screened to identify numerically important Chloroflexi genera. Fluorescence in situ hybridization probes were designed for their in situ characterization. All abundant Chloroflexi phylotypes were putatively identified as facultative anaerobic chemoorganotrophs involved in sugar fermentation. They were all filamentous but differed in their morphology and spatial arrangement. 'Candidatus Villigracilis' was predominantly located within the activated sludge flocs, where they possibly have structural importance, and their abundance was relatively stable. Conversely, the abundance of 'Candidatus Amarolinea' was highly dynamic, relative to other genera, sometimes reaching abundances in excess of 30% of the biovolume, suggesting their likely role in bulking episodes. This study gives an important insight into the role of Chloroflexi in WWTPs, thus contributing to the broader goal of understanding the ecology of these biotechnologically important systems.

Aims: The phylum Chloroflexi is frequently found in high abundance in methanogenic reactors, but their role is still unclear as most of them remain uncultured and understudied. Hence, a detailed analysis was performed in samples from five up-flow anaerobic sludge blanket (UASB) full-scale reactors fed different industrial wastewaters., Methods and Results: Quantitative PCR show that the phylum Chloroflexi was abundant in all UASB methanogenic reactors, with higher abundance in the reactors operated for a long period of time, which presented granular biomass. Both terminal restriction fragment length polymorphism and 16S rRNA gene amplicon sequencing revealed diverse Chloroflexi populations apparently determined by the different inocula. According to the phylogenetic analysis, the sequences from the dominant Chloroflexi were positioned in branches where no sequences of the cultured representative strains were placed. Fluorescent in situ hybridization analysis performed in two of the reactors showed filamentous morphology of the hybridizing cells., Conclusions: While members of the Anaerolineae class within phylum Chloroflexi were predominant, their diversity is still poorly described in anaerobic reactors. Due to their filamentous morphology, Chloroflexi may have a key role in the granulation in methanogenic UASB reactors., Significance and Impact of the Study: Our results bring new insights about the diversity, stability, dynamics and abundance of this phylum in full-scale UASB reactors which aid in understanding their function within the reactor biomass. However, new methodological approaches and analysis of bulking biomass are needed to completely unravel their role in these reactors. Combining all this knowledge with reactor operational parameters will allow to understand their participation in granulation and bulking episodes and design strategies to prevent Chloroflexi overgrowth., (© 2018 The Society for Applied Microbiology.)

Settleability of particles in activated sludge systems can be impaired by an overgrowth of filamentous bacteria, a problem known as bulking. These filaments are often members of the phylum Chloroflexi, sometimes reaching abundances in excess of 30% of the biovolume. The uncultured Chloroflexi phylotype, Candidatus Amarolinea, has been observed in high abundances in Danish full-scale activated sludge systems by 16S rRNA gene amplicon surveys, where it has been associated with bulking. In this study, fluorescence in situ hybridization was applied to confirm their high abundance, filamentous morphology, and contribution to the interfloc bridging that characterizes filamentous bulking. Furthermore, genome-centric metagenomics using both Illumina and Oxford Nanopore sequencing was used to obtain a near complete population genome (5.7Mbp) of the Ca. Amarolinea phylotype, which belongs to the proposed novel family Amarolineaceae within the order Caldilineales of Chloroflexi. Annotation of the genome indicated that the phylotype is capable of aerobic respiration, fermentation, and dissimilatory nitrate reduction to ammonia. The genome sequence also gives a better insight into the phylogenetic and evolutionary relationships of the organism. The name Candidatus Amarolinea aalborgensis is proposed for the species., (Copyright © 2018 The Authors. Published by Elsevier GmbH.. All rights reserved.)

Knowledge of connections between operational conditions, process stability, and microbial community dynamics is essential to enhance anaerobic digestion (AD) process efficiency and management. In this study, the detailed temporal effects of a sudden glycerol-based organic overloading on the AD microbial community and process imbalance were investigated in two replicate anaerobic digesters by a time-intensive sampling scheme. The microbial community time response to the overloading event was shorter than the shifts of reactor performance parameters. An increase in bacterial community dynamics and in the abundances of several microbial taxa, mainly within the Firmicutes, Tenericutes, and Chloroflexi phyla and Methanoculleus genera, could be detected prior to any shift on the reactor operational parameters. Reactor acidification already started within the first 24 h of the shock and headed the AD process to total inhibition in 72 h alongside with the largest shifts on microbiome, mostly the increase of Anaerosinus sp. and hydrogenotrophic methanogenic Archaea. In sum, this work proved that AD microbial community reacts very quickly to an organic overloading and some shifts occur prior to alterations on the performance parameters. The latter is very interesting as it can be used to improve AD process management protocols.

Herpetosiphon spp. are ubiquitous, chemoheterotrophic, filamentous gliding bacteria with the ability to prey on other microbes through a "wolf pack" mechanism. The genus currently comprises four known species ( H. aurantiacus , H. geysericola , H. giganteus , and H. gulosus ), which produce antimicrobial secondary metabolites such as siphonazole. As part of a study isolating myxobacterial wolf pack predators, we serendipitously isolated a novel environmental strain (CA052B) from the edge of a stream at Llansteffan, United Kingdom, which was identified as a member of the Herpetosiphon genus. A lawn culture method was utilized to analyze the predatory activity of CA052B against 10 prey organisms of clinical relevance. CA052B was found to prey on Escherichia coli , Klebsiella pneumoniae , Proteus mirabilis , Staphylococcus aureus , Staphylococcus epidermidis , Staphylococcus saprophyticus , Enterococcus faecalis , Bacillus subtilis , and Candida albicans Purified CA052B outer membrane vesicles also exhibited killing activity against the prey organisms when tested by flow cytometry. 16S rRNA sequencing of CA052B showed 98 to 99% identity with other Herpetosiphon species members. Comparing the genome of CA052B with the publicly available genomes of H. aurantiacus and H. geysericola revealed average nucleotide identities of only 84% and 91%, respectively, whereas the genome-to-genome distance calculation showed sequence identities of 28.2% and 46.6%, respectively. Biochemical characterization also revealed distinctions between CA052B and both H. gulosus and H. giganteus Thus, strain CA052B T (= DSM 107618 T = NBRC 113495 T ) is proposed to be the type strain of a novel species, Herpetosiphon llansteffanense sp. nov. The genome sequence of CA052B also revealed diverse secondary metabolite biosynthetic clusters, encouraging further exploration of its antibiotic production potential. IMPORTANCE Predatory bacteria are able to kill and consume other microbes and are therefore of interest as potential sources of new antimicrobial substances for applications in the clinic. "Wolf pack" predators kill prey by secreting antimicrobial substances into their surroundings, and those substances can kill prey organisms independently of the predatory cells. The genus Herpetosiphon exhibits wolf pack predation, yet its members are poorly described compared to other wolf pack predators, such as the myxobacteria. By providing a thorough characterization of a novel Herpetosiphon species, including its predatory, biochemical, and genomic features, this study increases our understanding of genomic variation within the Herpetosiphon genus and how that variation affects predatory activity. This will facilitate future rational exploitation of genus members (and other wolf pack predators) as sources of novel antimicrobials., (Copyright © 2018 Livingstone et al.)

Background: Representatives of the phylum Chloroflexi, though reportedly highly abundant in the extensive deep water habitats of both marine (SAR202 up to 30% of total prokaryotes) and freshwater (CL500-11 up to 26% of total prokaryotes), remain uncultivated and uncharacterized. There are few metagenomic studies on marine Chloroflexi representatives, while the pelagic freshwater Chloroflexi community is largely unknown except for a single metagenome-assembled genome of CL500-11., Results: Here, we provide the first extensive examination of the community composition of this cosmopolitan phylum in a range of pelagic habitats (176 datasets) and highlight the impact of salinity and depth on their phylogenomic composition. Reconstructed genomes (53 in total) provide a perspective on the phylogeny, metabolism, and distribution of three novel classes and two family-level taxa within the phylum Chloroflexi. We unraveled a remarkable genomic diversity of pelagic freshwater Chloroflexi representatives that thrive not only in the hypolimnion as previously suspected, but also in the epilimnion. Our results suggest that the lake hypolimnion provides a globally stable habitat reflected in lower species diversity among hypolimnion-specific CL500-11 and TK10 clusters in distantly related lakes compared to a higher species diversity of the epilimnion-specific SL56 cluster. Cell volume analyses show that the CL500-11 are among the largest prokaryotic cells in the water column of deep lakes and with a biomass to abundance ratio of two they significantly contribute to the deep lake carbon flow. Metabolic insights indicate participation of JG30-KF-CM66 representatives in the global cobalamin production via cobinamide to cobalamin salvage pathway., Conclusions: Extending phylogenomic comparisons to brackish and marine habitats suggests salinity as the major influencer of the community composition of the deep-dwelling Chloroflexi in marine (SAR202) and freshwater (CL500-11) habitats as both counterparts thrive in intermediate brackish salinity; however, freshwater habitats harbor the most phylogenetically diverse community of pelagic Chloroflexi representatives that reside both in epi- and hypolimnion.

Although neutral mine drainage is the less frequent subject of the interest than acid mine drainage, it can have adverse environmental effects caused mainly by precipitation of dissolved Fe. The aim of the study was to characterize the composition of bacterial population in environment with high concentration of iron and sulfur compounds represented by neutral mine drainage water of Elizabeth's shaft, Slovinky (Slovakia). Direct microscopic observations, cultivation methods, and 454 pyrosequencing of the 16S rRNA gene amplicons were used to examine the bacterial population. Microscopic observations identified iron-oxidizing Proteobacteria of the genera Gallionella and Leptothrix which occurrence was not changed during the years 2008-2014. Using 454 pyrosequencing, there were identified members of 204 bacterial genera that belonged to 25 phyla. Proteobacteria (69.55%), followed by Chloroflexi (10.31%) and Actinobacteria (4.24%) dominated the bacterial community. Genera Azotobacter (24.52%) and Pseudomonas (14.15%), followed by iron-oxidizing Proteobacteria Dechloromonas (11%) and Methyloversatilis (8.53%) were most abundant within bacterial community. Typical sulfur bacteria were detected with lower frequency, e.g., Desulfobacteraceae (0.25%), Desulfovibrionaceae (0.16%), or Desulfobulbaceae (0.11%). Our data indicate that the composition of bacterial community of the Elizabeth's shaft drainage water reflects observed neutral pH, high level of iron and sulfur ions in this aquatic habitat.

The dark ocean microbiota represents the unknown majority in the global ocean waters. The SAR202 cluster belonging to the phylum Chloroflexi was the first microbial lineage discovered to specifically inhabit the aphotic realm, where they are abundant and globally distributed. The absence of SAR202 cultured representatives is a significant bottleneck towards understanding their metabolic capacities and role in the marine environment. In this work, we use a combination of metagenome-assembled genomes from deep-sea datasets and publicly available single-cell genomes to construct a genomic perspective of SAR202 phylogeny, metabolism and biogeography. Our results suggest that SAR202 cluster members are medium sized, free-living cells with a heterotrophic lifestyle, broadly divided into two distinct clades. We present the first evidence of vertical stratification of these microbes along the meso- and bathypelagic ocean layers. Remarkably, two distinct species of SAR202 cluster are highly abundant in nearly all deep bathypelagic metagenomic datasets available so far. SAR202 members metabolize multiple organosulfur compounds, many appear to be sulfite-oxidizers and are predicted to play a major role in sulfur turnover in the dark water column. This concomitantly suggests an unsuspected availability of these nutrient sources to allow for the high abundance of these microbes in the deep sea.

The filamentous anoxygenic phototrophic bacterium Oscillochloris trichoides DG-6 has been studied, and it has been shown that there are no lipopolysaccharides on the cell surface. Fatty acids hydroxylated at the C3 position, amino sugars and phosphate-containing compounds characteristic of lipid A have also not been found. The genes encoding for proteins responsible for the synthesis of lipopolysaccharides and the genes for the transport system, usually localized in the outer membrane of Gram-negative bacteria, have not been detected in the genome. The rigid layer of the cell wall contains a peptidoglycan consisting of alanine, glutamine, ornithine and glycine, in the respective ratio 1.8 : 1.5 : 1.0 : 0.6. Thus, the investigated bacterium, Osc. trichoides, is a monoderm. The cell wall also contains a branched α-1,4-d-glucan with a repeating unit consisting of glucose residues linked by α-1→4 bonds (α-1→6 at the branching sites). Such polymers have not previously been reported in phototrophic bacteria.

A mesophilic, Gram-stain-positive, spore-forming bacterium that formed branched mycelia was isolated from paddy soil in Gunung Salak (Mount Salak), West Java, Indonesia. This strain, designated S-27T, grew at temperatures between 20 and 37 °C; the optimum growth temperature was 25 to 30 °C, and no growth was observed at 15 or 45 °C. The pH range for growth was pH 3.5 to 8.6; the optimum pH was 6.0, and no growth was observed at pH 3.0 or 9.2. Strain S-27T was able to hydrolyse polysaccharides such as starch, cellulose and xylan. The G+C content of the DNA of strain S-27T was 55.7 mol%. The major fatty acids were iso-C17 : 0 and C16 : 1 2-OH, and the major menaquinone was MK-9 (H2). The cell wall of strain S-27T contained d-glutamic acid, glycine, l-alanine, d-alanine, l-ornithine and β-alanine in a molar ratio of 1.0 : 1.6 : 1.4 : 0.6 : 0.9 : 1.1. The polar lipids consisted of phosphatidylglycerol, phosphatidylinositol and two glycolipids. The major cell-wall sugar was arabinose. Detailed phylogenetic analysis based on 16S rRNA gene sequences indicated that strain S-27T belongs to the order Ktedonobacterales and is most closely related to Ktedonobacter racemifer SOSP1-21T (89.6 % sequence identity). On the basis of its chemotaxonomic and phenotypic features and phylogenetic position, we concluded that strain S-27T represents a novel genus and species, for which we propose the name Dictyobacter aurantiacus gen. nov., sp. nov. The type strain of Dictyobacter aurantiacus is strain S-27T (=NBRC 109595T=InaCC B312T). Emendation of the description of the genus Thermosporothrix is also provided.

After the Chernobyl nuclear power plant accident in 1986, contaminated soils, vegetation from the Red Forest and other radioactive debris were buried within trenches. In this area, trench T22 has long been a pilot site for the study of radionuclide migration in soil. Here, we used 454 pyrosequencing of 16S rRNA genes to obtain a comprehensive view of the bacterial and archaeal diversity in soils collected inside and in the vicinity of the trench T22 and to investigate the impact of radioactive waste disposal on prokaryotic communities. A remarkably high abundance of Chloroflexi and AD3 was detected in all soil samples from this area. Our statistical analysis revealed profound changes in community composition at the phylum and OTUs levels and higher diversity in the trench soils as compared to the outside. Our results demonstrate that the total absorbed dose rate by cell and, to a lesser extent the organic matter content of the trench, are the principal variables influencing prokaryotic assemblages. We identified specific phylotypes affiliated to the phyla Crenarchaeota, Acidobacteria, AD3, Chloroflexi, Proteobacteria, Verrucomicrobia and WPS-2, which were unique for the trench soils., (© FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Background: Microbial reductive dechlorination of polychlorinated biphenyls (PCBs) plays a major role in detoxifying anoxic contaminated freshwater and marine sediments from PCBs. Known members of the phylum Chloroflexi are typically responsible for this activity in freshwater sediments, whereas less is known about the microorganisms responsible for this activity in marine sediments. PCB-respiring activities were detected in PCB-impacted marine sediments of the Venice Lagoon. The aim of this work was to identify the indigenous organohalide-respiring microorganisms in such environments and assess their dechlorination specificity against spiked Aroclor™ 1254 PCBs under laboratory conditions resembling the in situ biogeochemistry., Results: High PCB dechlorination activities (from 150 ± 7 to 380 ± 44 μmol of chlorine removed kg -1 week -1 ) were detected in three out of six sediments sampled from different locations of the lagoon. An uncultured non-Dehalococcoides phylotype of the class Dehalococcoidia closely related to Dehalobium chlorocoercia DF-1, namely phylotype VLD-1, was detected and enriched up to 10 9 16S rRNA gene copies per gram of sediment where dechlorination activities were higher and 25-4/24-4 and 25-2/24-2/4-4 chlorobiphenyls (CB) accumulated as the main tri-/dichlorinated products. Conversely, a different phylotype closely related to the SF1/m-1 clade, namely VLD-2, also enriched highly where lower dechlorination activity and the accumulation of 25-3 CB as main tri-chlorinated product occurred, albeit in the simultaneous presence of VLD-1. Both phylotypes showed growth yields higher or comparable to known organohalide respirers and neither phylotypes enriched in sediment cultures not exhibiting dechlorination., Conclusions: These findings confirm the presence of different PCB-respiring microorganisms in the indigenous microbial communities of Venice Lagoon sediments and relate two non-Dehalococcoides phylotypes of the class Dehalococcoidia to different PCB dechlorination rates and specificities.

Understanding the abundance change of certain bacterial taxa is quite important for the study of soil microbiology. However, the observed differences of relative abundances by high-throughput techniques may not accurately reflect those of the actual taxon abundances. This study investigated whether soil microbial abundances coupling with microbial quantities can be more informative in describing the microbial population distribution under different locations. We analyzed relative abundances of the major species in soil microbial communities from Beijing and Tibet grasslands by using 16 S rRNA high-throughput sequencing technique, and quantified the absolute bacterial cell numbers directly or indirectly by multiple culture-independent measurements, including adenosine tri-phosphate (ATP), flow cytometry (FCM), quantitative real-time PCR (qPCR), phospholipid fatty acids (PLFA) and microbial biomass Carbon (MBC). By comparison of the relative abundance and the estimated absolute abundances (EAA) of the major components in soil microbial communities, several dominant phyla, including Actinobacteria, Bacteroidetes, Verrucomicrobia, Chloroflexi, Gemmatimonates and Planctomycetes, showed significantly different trends. These results indicated that the change in EAA might be more informative in describing the dynamics of a population in a community. Further studies of soil microbes should combine the quantification and relative abundances of the microbial communities for the comparisons among various locations.

Chilas and Hunza areas, located in the Main Mantle Thrust and Main Karakoram Thrust of the Himalayas, host a range of geochemically diverse hot springs. This Himalayan geothermal region encompassed hot springs ranging in temperature from 60 to 95 °C, in pH from 6.2 to 9.4, and in mineralogy from bicarbonates (Tato Field), sulfates (Tatta Pani) to mixed type (Murtazaabad). Microbial community structures in these geothermal springs remained largely unexplored to date. In this study, we report a comprehensive, culture-independent survey of microbial communities in nine samples from these geothermal fields by employing a bar-coded pyrosequencing technique. The bacterial phyla Proteobacteria and Chloroflexi were dominant in all samples from Tato Field, Tatta Pani, and Murtazaabad. The community structures however depended on temperature, pH, and physicochemical parameters of the geothermal sites. The Murtazaabad hot springs with relatively higher temperature (90-95 °C) favored the growth of phylum Thermotogae, whereas the Tatta Pani thermal spring site TP-H3-b (60 °C) favored the phylum Proteobacteria. At sites with low silica and high temperature, OTUs belonging to phylum Chloroflexi were dominant. Deep water areas of the Murtazaabad hot springs favored the sulfur-reducing bacteria. About 40% of the total OTUs obtained from these samples were unclassified or uncharacterized, suggesting the presence of many undiscovered and unexplored microbiota. This study has provided novel insights into the nature of ecological interactions among important taxa in these communities, which in turn will help in determining future study courses in these sites.

Three filamentous gliding bacteria from the German Collection of Microorganisms and Cell Cultures, Hp g11, Hp g471 and Hp g472, were subjected to a phylogenetic analysis. These organisms had previously been classified as members of the genus Herpetosiphon based on their growth physiology and morphology. However, a taxonomic assignment at the species level had not been carried out. Analysis of 16S rRNA sequences now confirmed the close relationship of strain Hp g472 to Herpetosiphon aurantiacus DSM 785T (98.6 % nucleotide identity) and Herpetosiphon geysericola DSM 7119T (97.7 %). The results of DNA-DNA hybridization experiments further implied that strain Hp g472 should be classified as a distinct species. The DNA G+C content of strain Hp g472 was 49.9 mol%. The major quinone was MK-10 and the predominant cellular fatty acids were C18 : 1, C16 : 1 and C16 : 0. Based on phenotypic, chemotaxonomic and phylogenetic data it was concluded that strain Hp g472 represents a novel species of the genus Herpetosiphon, for which the name Herpetosiphon gulosus sp. nov. is proposed. The type strain is Hp g472T (=DSM 52871T=NBRC 112829T). In contrast to Hp g472T, the strains Hp g11 and Hp g471 exhibited closest 16S rRNA gene sequence similarity (>99 %) with 'Herpetosiphon giganteus' Hp a2. The distinctive genotypic and phenotypic properties of the latter supported the revival of the name as Herpetosiphon giganteus (ex Reichenbach & Golecki, 1975) sp. nov., nom. rev. We propose the previously deposited reference strain DSM 589T=NBRC 112828T as the type strain.