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In an acetate-fed anaerobic-aerobic membrane bioreactor with deteriorated enhanced biological phosphorus removal ( EBPR), D efluviicoccus-related tetrad-forming organisms ( DTFO) were observed to predominate in the microbial community. Using metagenomics, a partial genome of the predominant DTFO, ' C andidatus Defluviicoccus tetraformis strain TFO71', was successfully constructed and characterized. Examining the genome confirmed the presence of genes related to the synthesis and degradation of glycogen and polyhydroxyalkanoate ( PHA), which function as energy and carbon storage compounds. TFO71 and ' C andidatus Accumulibacter phosphatis' ( CAP) UW-1 and CAP UW-2, representative polyphosphate-accumulating organisms ( PAO), have PHA metabolism-related genes with high homology, but TFO71 has unique genes for PHA synthesis, gene regulation and granule management. We further discovered genes encoding DTFO polyphosphate ( polyP) synthesis, suggesting that TFO71 may synthesize polyP under untested conditions. However, TFO71 may not activate these genes under EBPR conditions because the retrieved genome does not contain all inorganic phosphate transporters that are characteristic of PAOs ( CAP UW-1, CAP UW-2, M icrolunatus phosphovorus NM-1 and T etrasphaera species). As a first step in characterizing EBPR-associated DTFO metabolism, this study identifies important differences between DTFO and PAO that may contribute to EBPR community competition and deterioration. [ABSTRACT FROM AUTHOR]

A low-diversity microbial community, dominated by the γ-proteobacterium H alomonas sulfidaeris, was detected in samples of warm saline formation porewater collected from the Cambrian Mt. Simon Sandstone in the Illinois Basin of the North American Midcontinent (1.8 km/5872 ft burial depth, 50° C, pH 8, 181 bars pressure). These highly porous and permeable quartz arenite sandstones are directly analogous to reservoirs around the world targeted for large-scale hydrocarbon extraction, as well as subsurface gas and carbon storage. A new downhole low-contamination subsurface sampling probe was used to collect in situ formation water samples for microbial environmental metagenomic analyses. Multiple lines of evidence suggest that this H. sulfidaeris-dominated subsurface microbial community is indigenous and not derived from drilling mud microbial contamination. Data to support this includes V1- V3 pyrosequencing of formation water and drilling mud, as well as comparison with previously published microbial analyses of drilling muds in other sites. Metabolic pathway reconstruction, constrained by the geology, geochemistry and present-day environmental conditions of the Mt. Simon Sandstone, implies that H. sulfidaeris-dominated subsurface microbial community may utilize iron and nitrogen metabolisms and extensively recycle indigenous nutrients and substrates. The presence of aromatic compound metabolic pathways suggests this microbial community can readily adapt to and survive subsurface hydrocarbon migration. [ABSTRACT FROM AUTHOR]

Strain MS-P2T was isolated from microbial mats associated with Mushroom Spring, an alkaline siliceous hot spring in Yellowstone National Park, WY, USA. The isolate grows chemoheterotrophically by oxygen-dependent respiration, and light stimulates photoheterotrophic growth under strictly oxic conditions. Strain MS-P2T synthesizes bacteriochlorophyll a and the carotenoid spirilloxanthin. However, photoautotrophic growth did not occur under oxic or anoxic conditions, suggesting that this strain should be classified as an aerobic anoxygenic phototrophic bacterium. Strain MS-P2T cells are motile, curved rods about 0.5 to 1.0 μm wide and 1.0 to 1.5 μm long. The optimum growth temperature is 45–50 °C, and the optimum pH for growth is circum-neutral (pH 7.0–7.5). Sequence analysis of the 16S rRNA gene revealed that strain MS-P2T is closely related to Elioraea species, members of the class Alphaproteobacteria, with a sequence identity of 96.58 to 98%. The genome of strain MS-P2T is a single circular DNA molecule of 3,367,643 bp with a mol% guanine-plus-cytosine content of 70.6%. Based on phylogenetic, physiological, biochemical, and genomic characteristics, we propose this bacteriochlorophyll a-containing isolate is a new species belonging to the genus Elioraea, with the suggested name Elioraeatepida. The type-strain is strain MS-P2T (= JCM33060T = ATCC TSD-174T). [ABSTRACT FROM AUTHOR]

The anaerobic free-living ciliate, Trimyema compressum, is known to harbor both methanogenic archaeal and bacterial symbionts in the cytoplasm. To clarify their phylogenetic belongings, a full-cycle rRNA approach was applied to this symbiosis. Phylogenetic analysis showed that the methanogenic symbiont was related to Methanobrevibacter arboriphilicus, which was distantly related to symbionts found in other Trimyema species. This result suggested that Trimyema species do not require very specific methanogenic symbionts, and symbiont replacement could have occurred in the history of Trimyema species. On the other hand, the bacterial symbiont was located near the lineage of the family Syntrophomonadaceae in the phylum Firmicutes. The sequence similarity between the bacterial symbiont and the nearest species was 85%, indicating that bacterial symbionts may be specific to the Trimyema species. The elimination of bacterial symbionts from the ciliate cell by antibiotic treatment resulted in considerably decreased host growth. However, it was not restored by stigmasterol addition (<2 μg ml−1), which was different from the previous report that showed that the symbiont-free strain required exogenous sterols for growth. In addition, the decline of host growth was not accompanied by host metabolism shift toward the formation of more reduced products, which suggested that the contribution of bacterial symbionts to the host ciliate was not a dispose of excessive reducing equivalent arising from the host’s fermentative metabolism as methanogenic symbionts do. This study showed that bacterial symbionts make a significant contribution to the host ciliate by an unknown function and suggested that interactions between bacterial symbionts and T. compressum are more complicated than hitherto proposed. [ABSTRACT FROM AUTHOR]

The article investigates the influence of carbon sources on bacterial community structure in the gut of the wood-feeding higher termite Nasutitermes takasogoensis. It reveals that the bacterial community structure changed markedly depending on feed components at the phylum level. The article examines the symbiotic relationship between termite and gut microorganisms.

Commercially available MgB2 powders were consolidated into bulk samples by two different shock wave consolidation methods: underwater shock consolidation method and gun method. Resistance vs. temperature of the samples was measured by the four-terminal method for pulsed currents of up to 3 A in self-field, as well as Vickers hardness, SEM micrographs of fraction surfaces, packing densities, and X-ray diffraction patterns. These results, in comparison with cold isostatic pressed samples, indicated that the underwater shock consolidated sample was superior in grain connectivity to the others. This is probably because the underwater shock consolidation generated most anisotropic and hence high frictional, compressive, intergrain forces. [Copyright &y& Elsevier]

H2 is an important fermentation intermediate in anaerobic environments. Although H2 occurs at very low partial pressures in the environments, the culture and isolation of H2-utilizing microorganisms is usually carried out under very high H2 pressures, which might have hampered the discovery and understanding of microorganisms adapting to low H2 environments. Here we constructed a culture system designated the "iron corrosion-assisted H2-supplying (iCH) system" by connecting the gas phases of two vials (one for the iron corrosion reaction and the other for culturing microorganisms) to achieve cultures of microorganisms under low H2 pressures. We conducted enrichment cultures for methanogens and acetogens using rice paddy field soil as the microbial source. In the enrichment culture of methanogens under canonical high H2 pressures, only Methanobacterium spp. were enriched. By contrast, Methanocella spp. and Methanoculleus spp., methanogens adapting to low H2 pressures, were specifically enriched in the iCH cultures. We also observed selective enrichment of acetogen species by the iCH system (Acetobacterium spp. and Sporomusa spp.), whereas Clostridium spp. predominated in the high H2 cultures. These results demonstrate that the iCH system facilitates culture of anaerobic microorganisms under low H2 pressures, which will enable the selective culture of microorganisms adapting to low H2 environments. [ABSTRACT FROM AUTHOR]

Background/aims: The gut virome is mainly composed of bacteriophages and influences gut homeostasis and pathogenic conditions. In this study, we analyzed the gut prokaryotic virome in Japanese patients with Crohn's disease (CD). Materials/methods: We collected 19 fecal samples from CD patients and 16 samples from healthy controls. The gut bacteriome was analyzed by 16S rRNA gene sequencing and the virome was profiled by shotgun metagenomic sequencing. Results: Despite no differences in richness and evenness, there was a significant difference in the overall structure of the gut virome between CD patients and controls (P = 0.013). CrAssphage and Staphylococcus virus, belonging to the order Caudovirales, were dominant in the gut virome of controls and CD patients. The abundance of crAssphage was significantly greater in CD patients than controls (P = 0.021). Lactococcus, Enterococcus and Lactobacillus phages were present only in CD patients, while Xanthomonas and Escherichia phages were unique to the controls. In the gut bacteriome of CD patients, richness and evenness were significantly lower, and a significant difference in the overall structure was observed between groups (P = 0.014). The gut bacteriome of CD patients was characterized by a decrease of the genera Faecalibacterium, Roseburia, and Ruminococcus and an increase of the family Enterobacteriaceae. There were more significant correlations between viruses and bacteria in CD patients than controls. Conclusions: The gut virome of CD patients was distinct from that of healthy controls in a Japanese population. An altered gut virome may be one of the factors associated with the bacterial dysbiosis of CD. [ABSTRACT FROM AUTHOR]

Sclerotia were formed in agar culture by a fungus with clamp connections isolated from rice husks at Tsukuba, Japan. The sclerotia were brown, globose to ellipsoidal, small, up to 200 μm in diameter, and composed of external rind tissue and internal medulla tissue. Such tiny sclerotia have not been commonly reported among basidiomycetous fungi in the literature. The fungus was identified as Coprinopsis cinerea on the basis of morphological characteristics together with molecular analyses. Three reference strains of C. cinerea formed sclerotia similarly under identical cultural conditions. [ABSTRACT FROM AUTHOR]

Microbial diversity and methanogenic potential in formation water samples from a dissolved-in-water type gas field were investigated by using 16S rRNA gene libraries and culture-based methods. Two formation water samples (of 46 and 53°C in temperature) were obtained from a depth of 700 to 800 m. Coenzyme F420-autofluorescence indicated that 103–104 cells per ml of active methanogens were present, accounting for at least 10% of the total cell count. The 16S rRNA gene sequence analysis indicated that the diversity of Archaea and Bacteria of the two samples was quite limited; i.e., the archaeal libraries were dominated by the sequences related to Methanobacterium formicicum and Methanothermobacter thermautotrophicus, and the bacterial libraries were dominated by the sequences related to Hydrogenophilus and Deferribacter. Of the methanogenic substrates tested using the formation water-based medium, only H2–CO2 gave rise to methane formation. Those dominant archaeal and bacterial genera have the potential to use hydrogen for growth at the in situ temperatures, suggesting that the formation water of the Pliocene strata in the gas field has been provided with hydrogen, probably from underneath the strata, and thus on-going active methanogenesis has been occurring to date. [ABSTRACT FROM AUTHOR]

Microbial potential of crude oil degradation coupled to methane production has attracted much attention as a basis for microbial enhanced energy recovery (MEER) technology. Here we performed laboratory incubation experiments mimicking in situ temperature and pressure conditions of subsurface oil reservoirs to evaluate the effectiveness of biological augmentation and stimulation for MEER. Using our high temperature and pressure incubation system, we successfully obtained a microbial community capable of methanogenic crude oil degradation from the Yamagata oil reservoir in Japan. To evaluate the potential of biological augmentation, we inoculated the microbial culture from Yamagata into production water from the Akita oil reservoir in which the indigenous microbial community cannot degrade crude oil. We observed methane production associated with toluene degradation, indicating that biological augmentation could be successful. We also evaluated the potential of biological stimulation, i.e. the effects of supplementing with different nutrients on crude oil degradation using the Yamagata oil reservoir sample. Intriguingly, addition of specific yeast extracts (YEs) resulted in notably enhanced methane production associated with the degradation of longer-chain n -alkanes as well as toluene. We further assessed the effectiveness of combining the biological augmentation and stimulation by inoculating the microbial culture from Yamagata together with the effective YE into the Akita production water, and found a large amount of methane production coupled to toluene and n -alkane degradation during the incubation. Taken together, our results suggest that the bio-augmentation and stimulation strategies demonstrated here could be a powerful tool for energy recovery from petroleum reservoirs both with and without innate crude oil degradation. [Display omitted] • Methanogenic microbial community capable of crude oil degradation was obtained. • Microbial community injection into oil reservoirs could induce crude oil degradation. • Nutrients stimulating methanogenic n -alkane degradation were discovered. [ABSTRACT FROM AUTHOR]

Anaerobic microbial acetogenesis is ubiquitous on Earth, and thus plays an important role in the global carbon cycle. The mechanism of carbon fixation in acetogens has attracted great interest from various studies for combatting climate change, and even for studying ancient metabolic pathways. Here, we developed a new, simple method for investigating carbon flows in the metabolic reaction of acetogen by conveniently and accurately determining the relative abundance of individual acetate- and/or formate-isotopomers formed in 13C labeling experiments. We measured the underivatized analyte by gas chromatography-mass spectrometry (GC-MS) coupled with a direct aqueous sample injection technique. The individual abundance of analyte isotopomers was calculated by the mass spectrum analysis using the least-squares approach. The validity of the method was demonstrated by determining known mixtures of unlabeled and 13C-labeled analytes. The developed method was applied to study the carbon fixation mechanism of the well-known acetogen Acetobacterium woodii grown on methanol and bicarbonate. We provided a quantitative reaction model for methanol metabolism of A. woodii , which indicated that methanol was not the sole carbon precursor of the acetate methyl group and that 20−22% of the methyl group was formed from CO 2. In contrast, the carboxyl group of acetate appeared to form exclusively by CO 2 fixation. Thus, our simple method, without laborious analytical procedures, has broad utility for the study of biochemical and chemical processes related to acetogenesis on Earth. [Display omitted] • A new method for quantifying 13C distribution in acetate and formate was developed. • GC-MS method coupled with the MS spectra analysis using a least-squares approach. • The method was applied to study carbon flow in methanol metabolism of acetogen. • Quantitative reaction model indicated that 20% of acetate methyl was derive from CO 2. [ABSTRACT FROM AUTHOR]

Methane (CH 4) associated with marine and terrestrial sites of serpentinization has been proposed to be abiotic in origin. However, the source of carbon and the depth and temperature of CH 4 synthesis often remain inconclusive. We measured the radiocarbon (14C), bulk stable isotope ratios (δ 13 C and δ D) and isotopologue abundance (Δ 13 CH 3 D) of CH 4 , and noble gas isotope composition of gas samples from two hyperalkaline geothermal wells (Happo #1 and Happo #3) at Hakuba Happo, Japan, to constrain the source of carbon and the CH 4 generation processes. The CH 4 samples from both sites were nearly 14C-free, whereas the carbonate precipitates inside the Happo #1 well contained 14C corresponding to 51 to 62 percent modern carbon, indicating that the majority of CH 4 was not generated from the reduction of dissolved carbonate in the hot spring water. CH 4 samples from Happo #1 and Happo #3 yielded Δ 13 CH 3 D-based apparent temperatures of 206 − 40 + 52 °C and 323 − 85 + 143 °C, respectively, which are much higher than the measured well water temperatures (∼50 °C). Therefore, 14C and clumped isotopologue temperatures suggest that Hakuba Happo CH 4 was generated below the depth where the shallow meteoric water circulated. The 3He/4He ratios were 4.10 and 4.47 R atm for Happo #1 and Happo #3, respectively. The 3He/4He and 4He/20Ne ratios revealed that approximately 50% of He was of mantle origin, suggesting that the Hakuba Happo hot spring received volatiles, including CO 2 , from the mantle. However, the observed δ 13 C CH4 values (approximately −35‰) were significantly lower than those of typical mantle-derived carbon (–5‰), implying that mantle-derived CO 2 is not the major carbon source for CH 4 formation. High CH 4 concentrations in the Hakuba Happo fluids, compared to those in hot springs in the area not associated with serpentinization, suggest that CH 4 was generated from 13C-depleted fossil carbon sources and serpentinization-derived H 2 at high temperatures (>200 °C), and subsequently entrained into the cooler circulating meteoric water system. • 14C, Δ 13 CH 3 D, δ 13 C, δ D and noble gas isotope constraints on the origin of CH 4. • CH 4 is formed at deep region isolated from meteoric water circulation. • CH 4 can be formed from 13C depleted fossil carbon with serpentinization derived H 2. [ABSTRACT FROM AUTHOR]

Some 25 fungi, including at least 14 basidiomycetes, one ascomycete, and five anamorphic fungi were evaluated for their cellulose-degrading abilities in Difco potato dextrose broth or Difco malt extract broth cultures with cellulosic substrates (e.g., filter paper) in plastic Petri dishes. Among them, Peniophora sp. 06-13 and Phlebia sp. 99-335 reduced the dry weights of the whole cultures with these substrates more than the dry weights of the respective original substrates after 30 days of culture, showing definite cellulose degradation. In the cultures with more than 10 test fungi including Pycnoporus coccineus 84-117, such weight losses did not occur. This assay technique for the primary screening for cellulose degrading fungi is simple, inexpensive, reproducible and accurate. [ABSTRACT FROM AUTHOR]

Summary Anaerobic methane-oxidizing archaea (ANME) are known to play an important role in methane flux, especially in marine sediments. The 16S rRNA genes of ANME have been detected in terrestrial freshwater subsurfaces. However, it is unclear whether ANME are actively involved in methane oxidation in these environments. To address this issue, Holocene sediments in the subsurface of the Kanto Plain in Japan were collected for biogeochemical and molecular analysis. The potential activity of the anaerobic oxidation of methane (AOM) (0.38-3.54 nmol cm−3 day−1) was detected in sediment slurry incubation experiments with a 13CH4 tracer. Higher AOM activity was observed in low-salinity treatment compared with high-salinity condition (20‰), which supports the adaptation of ANME in freshwater habitats. The 16S rRNA sequence analysis clearly revealed the presence of a distinct subgroup of ANME-1, designated ANME-1a-FW. Phylogenetic analysis of the mcrA genes also implied the presence of the distinct subgroup in ANME-1. ANME-1a-FW was found to be the most dominant active group in the archaeal communities on the basis of 16S rRNA analysis (75.0-93.8% of total archaeal 16S rRNA clones). Sulfate-reducing bacteria previously known as the syntrophic bacterial partners of ANME-1 was not detected. Our results showed that ANME-1a-FW is adapted to freshwater habitats and is responsible for AOM in terrestrial freshwater subsurface environments. [ABSTRACT FROM AUTHOR]

Abstract: Three different cylindrical MgB2 bulk samples were prepared by the underwater shock consolidation method in which shock waves of several GPa, generated by detonation of explosives, were applied to a metallic cylinder containing commercially available MgB2 powders with no additives. Resistivity anisotropy of the samples increased with shock pressure. The highest- and medium-pressure applied samples had finite resistivities in the radial direction for the whole temperature range down to 12K, whereas their axial and azimuthal resistivities dropped to zero at 32–35K. By contrast, the lowest-pressure applied sample was approximately isotropic with a normal-state resistivity of ∼40μΩcm, an onset temperature of ∼38.5K, and a transition width of ∼4.5K. These extremely anisotropic properties would have resulted from the distortion of grain boundaries and grain cores, caused by the shock pressures and their repeated bouncing. [Copyright &y& Elsevier]

We previously showed that novel filterable bacteria remain in "sterile" (<0.2 μm filtered) terrestrial environmental samples from Japan, China, and Arctic Norway. Here, we characterized the novel filterable strain IZ6T, a representative strain of a widely distributed lineage. Phylogenetic analysis showed that this strain was affiliated with the Rhizobiales (now proposed as Hyphomicrobiales) of Alphaproteobacteria, but distinct from any other type strains. Strain IZ6T shared the following chemotaxonomic features with the closest (but distantly) related type strain, Flaviflagellibacter deserti SYSU D60017T: ubiquinone-10 as the major quinone; phosphatidylethanolamine, phosphatidylcholine, and phosphatidylglycerol as major polar lipids; and slightly high G+C content of 62.2 mol%. However, the cellular fatty acid composition differed between them, and the unsaturated fatty acid (C18:1ω7c/C18:1ω6c) was predominantly found in our strain. Moreover, unlike methyrotrophs and nitrogen-fixers of the neighboring genera of Hyphomicrobiales (Rhizobiales), strain IZ6T cannot utilize a one-carbon compound (e.g., methanol) and fix atmospheric nitrogen gas. These findings were consistent with the genome-inferred physiological potential. Based on the phylogenetic, physiological, and chemotaxonomic traits, we propose that strain IZ6T represents a novel genus and species with the name Terrihabitans soli gen. nov., sp. nov. (=NBRC 106741T = NCIMB 15058T). The findings will provide deeper insight into the eco-physiology of filterable microorganisms. [ABSTRACT FROM AUTHOR]

Natural microbial communities consist of a limited number of abundant species and an extraordinarily diverse population of rare species referred to as the rare biosphere. Recent studies have revealed that the rare biosphere is not merely an inactive dormant population but may play substantial functional roles in the ecosystem. However, structure, activity and community assembly processes of the rare biosphere are poorly understood. In this study, we evaluated the present and living microbial community structures including rare populations in an aquifer ecosystem, the Mahomet Aquifer, USA, by both 16S rDNA and rRNA amplicon deep sequencing. The 13 groundwater samples formed three distinct groups based on the "entire" community structure, and the same grouping was obtained when focusing on the "rare" subcommunities (<0.1% of total abundance), while the "abundant" subcommunities (>1.0%) gave a different grouping. In the correlation analyses, the observed grouping pattern is associated with several geochemical factors, and structures of not only the entire community but also the rare subcommunity are correlated with geochemical profiles in the aquifer ecosystem. Our findings first indicate that the living rare biosphere in the aquifer system has the metabolic potential to adapt to local geochemical factors which dictate the community assembly processes. [ABSTRACT FROM AUTHOR]

Crop rotation and intercropping with Allium plants suppresses Fusarium wilt in various crops. However, the mechanisms underlying this phenomenon have not been fully elucidated. This study was designed to assess the role of microorganisms inhabiting Allium rhizospheres and antifungal compounds produced by Allium roots in Fusarium wilt suppression by Allium cultivation. Suppression of cucumber Fusarium wilt and the pathogen multiplication by Allium (Welsh onion and/or onion)-cultivated soils were eliminated by heat treatment at 60 °C, whereas those by Welsh onion-root extract were lost at 40 °C. The addition of antibacterial antibiotics eliminated the suppressive effect of Welsh onion-cultivated soil on pathogen multiplication, suggesting the contribution of antagonistic gram-negative bacteria to the soil suppressiveness. The Illumina MiSeq sequencing of 16S rRNA gene amplicons revealed that genus Flavobacterium was the predominant group that preferentially accumulated in Allium rhizospheres. Flavobacterium species recovered from the rhizosphere soils of these Allium plants suppressed Fusarium wilt on cucumber seedlings. Furthermore, confocal laser scanning microscopy revealed that Flavobacterium isolates inhibited the multiplication of the pathogen in soil. Taken together, we infer that the accumulation of antagonistic Flavobacterium species plays a key role in Fusarium wilt suppression by Allium cultivation. [ABSTRACT FROM AUTHOR]

A Gram-negative, obligatory anaerobic, chemoheterotrophic bacterium, designated strain IA91 T , was isolated from sediments and formation water from deep aquifers in Japan. IA91 T derives its peptidoglycan, energy and carbon from exogenous cell wall fragments, namely muropeptides, released from actively reproducing bacteria, and is dependent on other bacteria for cell wall formation, growth and even cell shape: IA91 T is irregular rod-shaped but coccoids when muropeptide is absent. IA91 T grew in a temperature range of 25-45 °C with optimum growth at 40 °C. IA91 T utilized limited substrates, yeast extract, muropeptides and d-lactate. The major end products from yeast extract degradation were acetate, hydrogen and carbon dioxide. Co-cultivation with a hydrogen-scavenging methanogenic archaeon promoted IA91 T growth. No anaerobic respiration with nitrate, nitrite, sulphate or Fe(III) was observed. The major cellular fatty acids are C16 : 0, C18 : 1 trans 9, C18 : 0 and C17 : 0. The G+C content of the genomic DNA was 45.6 mol%. Phylogenetic analysis based on 16S rRNA gene and conserved protein sequences involved in replication, transcription and translation indicated that IA91 T belonged to the candidate phylum Marine Group A (MG-A, SAR406 or Ca . Marinimicrobia) with no cultivated representatives. Based on the phenotypic and phylogenomic characteristics, a new genus and species, Fidelibacter multiformis gen. nov., sp. nov., is proposed for IA91 T (= JCM 39387 T = KCTC 25736 T ). In addition, a new bacterial phylum named Fidelibacterota phyl. nov. is proposed for the candidate phylum MG-A represented by F. multiformis and Fidelibacteraceae fam. nov., Fidelibacterales ord. nov. and Fidelibacteria classis nov.

Most of Earth's prokaryotes live under energy limitation, yet the full breadth of strategies that enable survival under such conditions remain poorly understood. Here we report the isolation of a bacterial strain, IA91, belonging to the candidate phylum Marine Group A (SAR406 or 'Candidatus Marinimicrobia') that is unable to synthesize the central cell wall compound peptidoglycan itself. Using cultivation experiments and microscopy, we show that IA91 growth and cell shape depend on other bacteria, deriving peptidoglycan, energy and carbon from exogenous muropeptide cell wall fragments released from growing bacteria. Reliance on exogenous muropeptides is traceable to the phylum's ancestor, with evidence of vertical inheritance across several classes. This dependency may be widespread across bacteria (16 phyla) based on the absence of key peptidoglycan synthesis genes. These results suggest that uptake of exogenous cell wall components could be a relevant and potentially common survival strategy in energy-limited habitats like the deep biosphere., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)

A novel anaerobic, thermophilic bacterium of the class Atribacteria, strain M15 T , was isolated from a high-temperature gas reservoir, Japan. Cells of strain M15 T were gram-negative, short oval-shaped, and lacked flagella. Growth occurred at 45-75 °C (optimum 70-75 °C) and pH 6.5-8.5 (optimum pH 7.5-8.0) and was fast under optimal conditions (doubling time 11.4 h). Yeast extract was required for growth. Fermentative growth with glucose, arabinose, xylose, and cellobiose was observed. The major fermentative end products of glucose were acetate and hydrogen. The major cellular fatty acids were C 16:0 , iso-C 15:0 , and C 18:0 . The genomic G + C content was 46.0 mol%. Fluorescence and electron microscopy observations revealed the intracellular localization of genomic DNA surrounded by a membrane in the cells of strain M15 T as reported in a sole validly described species of the class Atribacteria in the phylum Atribacterota, Atribacter laminatus strain RT761 T , suggesting that the unique morphological traits are widely shared in this class. Phylogenetic analyses indicated that strain M15 T belongs to a distinct family-level lineage in the class Atribacteria and shows low similarities to Atribacter laminatus strain RT761 T (16S rRNA gene sequence identity of 90.1 %, average nucleotide identity [ANI] of 66.1 %, average amino acid identity [AAI] of 55.8 %). Phenotypic traits of strain M15 T (thermophilic, fast-growing, relatively high G + C content, etc.) were clearly distinct from A. laminatus. Based on these phenotypic and genomic properties, we propose a novel genus and species, Atrimonas thermophila gen. nov., sp. nov. for strain M15 T (=JCM39389 T , =KCTC25731 T ) representing a novel family Atrimonadaceae fam., nov. in the class Atribacteria., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier GmbH.. All rights reserved.)

Our previous studies indicate the abundant and diverse presence of yet-to-be-cultured microorganisms in the micropore-filtered fractions of various environmental samples. Here, we isolated a novel bacterium (designated as strain TMPK1T) from a 0.45-μm-filtered soil suspension by using a gel-filled microwell array device comprising 900 microwells and characterized its phylogenetic and physiological features. This strain showed low 16S rRNA gene sequence identities (<91%) and low average nucleotide identity values (<70%) to the closest validly described species, and belonged to a novel-family-level lineage within the order Rhodospirillales of Alphaproteobacteria. Strain TMPK1T exhibited small cell sizes (0.08-0.23 μm3) and had a high cyclopropane fatty acid content (>13%), and these characteristics were differentiated from other Rhodospirillales bacteria. A comprehensive habitability search using amplicon datasets suggested that TMPK1T and its close relatives are mainly distributed in soil and plant-associated environments. Based on these results, we propose that strain TMPK1T represents a novel genus and species named Roseiterribacter gracilis gen. nov., sp. nov. (JCM 34627T = KCTC 82790T). We also propose Roseiterribacteraceae fam. nov. to accommodate the genus Roseiterribacter., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Nakai et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

The "duckweed-microbes co-cultivation method" is a microbial isolation technique that effectively recovers diverse microbes, including rarely cultivated bacterial phyla, from environmental samples. In this method, aseptic duckweed and microbes collected from an environmental sample are co-cultivated for several days, and duckweed-associated microbes are then isolated from its roots using a conventional agar plate-based cultivation method. We herein propose several improvements to the method in order to specifically obtain members of the rarely cultivated bacterial phylum, Verrucomicrobiota. In systems using river water as the inoculum, the marked enrichment of Verrucomicrobiota was observed after 10 days of co-cultivation, particularly in the roots and co-cultivated media. We also successfully isolated 44 strains belonging to subdivisions 1, 3, and 4 of the phylum Verrucomicrobiota from these systems. This was achieved by changing the concentration of nitrogen in the co-cultivation medium, which is known to affect duckweed growth and/or metabolism, and by subjecting the fronds and co-cultivated media as well as the roots after co-cultivation to microbial isolation.

The cycle of life and death and Earth's carbon cycle(s) are intimately linked, yet how bacterial cells, one of the largest pools of biomass on Earth, are recycled back into the carbon cycle remains enigmatic. In particular, no bacteria capable of scavenging dead cells in oxygen-depleted environments have been reported thus far. In this study, we discover the first anaerobes that scavenge dead cells and the two isolated strains use distinct strategies. Based on live-cell imaging, transmission electron microscopy, and hydrolytic enzyme assays, one strain (designated CYCD) relied on cell-to-cell contact and cell invagination for degrading dead food bacteria where as the other strain (MGCD) degraded dead food bacteria via excretion of lytic extracellular enzymes. Both strains could degrade dead cells of differing taxonomy (bacteria and archaea) and differing extents of cell damage, including those without artificially inflicted physical damage. In addition, both depended on symbiotic metabolic interactions for maximizing cell degradation, representing the first cultured syntrophic Bacteroidota. We collectively revealed multiple symbiotic bacterial decomposition routes of dead prokaryotic cells, providing novel insight into the last step of the carbon cycle., (© 2023. The Author(s), under exclusive licence to International Society for Microbial Ecology.)

Deciphering unclear microbial interactions is key to improving biological wastewater treatment processes. Microbial predation and parasitism in wastewater treatment ecosystems are unexplored survival strategies that have long been known and have recently attracted attention because these interspecies interactions may contribute to the reduction of excess sludge. Here, microbial community profiling of 600 activated sludge samples taken from six industrial and one municipal wastewater treatment processes (WWTPs) was conducted. To identify the shared lineages in the WWTPs, the shared microbial constituents were defined as the family level taxa that had ≥ 0.1% average relative abundance and detected in all processes. The microbial community analysis assigned 106 families as the shared microbial constituents in the WWTPs. Correlation analysis showed that 98 of the 106 shared families were significantly correlated with total carbon (TC) and/or total nitrogen (TN) concentrations, suggesting that they may contribute to wastewater remediation. Most possible predatory or parasitic bacteria belonging to the phyla Bdellovibrionota, Myxococcota, and Candidatus Patescibacteria were found to be the shared families and negatively correlated with TC/TN; thus, they were frequently present in the WWTPs and could be involved in the removal of carbon/nitrogen derived from cell components. Shotgun metagenome-resolved metabolic reconstructions indicated that gene homologs associated with predation or parasitism are conserved in the Bdellovibrionota, Myxococcota, and Ca . Patescibacteria genomes ( e.g. , host interaction (hit) locus, Tad-like secretion complexes, and type IV pilus assembly proteins). This study provides insights into the complex microbial interactions potentially linked to the reduction of excess sludge biomass in these processes., Competing Interests: The authors declare that they have no competing financial interests or personal relationships that may have influenced the work reported in this study., (© 2023 The Authors. Published by Elsevier Ltd.)

We report a complete genome sequence of Dyella sp. strain GSA-30, a predominant endophytic bacterium of Dendrobium plants. The genome consists of a circular 5,501,810-bp chromosome with a G+C content of 61.4%. The genome was predicted to harbor 6 rRNA genes, 51 tRNA genes, and 4,713 coding sequences.

Here, we report a complete genome sequence of Flavobacterium sp. strain GSB-24, an endophytic bacterium of Dendrobium plants. The genome consists of a circular 5,286,830-bp chromosome with a G+C content of 33.8% and a circular 64,374-bp plasmid with a G+C content of 29.3%.

We herein propose a fast and easy DNA and RNA co-extraction method for environmental microbial samples. It combines bead beating and phenol-chloroform phase separation followed by the separation and purification of DNA and RNA using the Qiagen AllPrep DNA/RNA mini kit. With a handling time of ~3 h, our method simultaneously extracted high-quality DNA (peak size >10-15‍ ‍kb) and RNA (RNA integrity number >6) from lake bacterioplankton filtered samples. The method is also applicable to low-biomass samples (expected DNA or RNA yield <50‍ ‍ng) and eukaryotic microbial samples, providing an easy option for more versatile eco-genomic applications.

Serpentinization of ultramafic rocks provides molecular hydrogen (H 2 ) that can support lithotrophic metabolism of microorganisms, but also poses extremely challenging conditions, including hyperalkalinity and limited electron acceptor availability. Investigation of two serpentinization-active systems reveals that conventional H 2 -/CO 2 -dependent homoacetogenesis is thermodynamically unfavorable in situ due to picomolar CO 2 levels. Through metagenomics and thermodynamics, we discover unique taxa capable of metabolism adapted to the habitat. This included a novel deep-branching phylum, "Ca. Lithacetigenota", that exclusively inhabits serpentinite-hosted systems and harbors genes encoding alternative modes of H 2 -utilizing lithotrophy. Rather than CO 2 , these putative metabolisms utilize reduced carbon compounds detected in situ presumably serpentinization-derived: formate and glycine. The former employs a partial homoacetogenesis pathway and the latter a distinct pathway mediated by a rare selenoprotein-the glycine reductase. A survey of microbiomes shows that glycine reductases are diverse and nearly ubiquitous in serpentinite-hosted environments. "Ca. Lithacetigenota" glycine reductases represent a basal lineage, suggesting that catabolic glycine reduction is an ancient bacterial innovation by Terrabacteria for gaining energy from geogenic H 2 even under hyperalkaline, CO 2 -poor conditions. Unique non-CO 2 -reducing metabolisms presented here shed light on potential strategies that extremophiles may employ for overcoming a crucial obstacle in serpentinization-associated environments, features potentially relevant to primordial lithotrophy in early Earth., (© 2022. The Author(s).)

Dendrobium plants are members of the family Orchidaceae , many of which are endangered orchids with ornamental and medicinal values. Dendrobium endophytic microbes have attracted attention for the development of strategies for plant protection and utilization of medicinal principles. However, the role of endophytic bacteria is poorly elucidated due to the lack of their successful cultivation. This study obtained a total of 749 endophytic isolates from Dendrobium roots using solid media prepared by simply modified methods (separate sterilization of phosphate and agar [PS] and use of gellan gum as a gelling reagent [GG]) and by a conventional method of autoclaving the phosphate and agar together (PT method). Notably, based on a comparison of 16S rRNA gene sequences between the isolates and the Dendrobium root endophyte community, we successfully retrieved more than 50% (17 out of 30) of the predominant endophytic bacterial operational taxonomic units (OTUs) using PS and GG media, which is a much higher recovery rate than that of PT medium (16.7%). We further found that a number of recalcitrant bacteria, including phylogenetically novel isolates and members of even the rarely cultivated phyla Acidobacteriota and Verrucomicrobiota , were obtained only when using PS and/or GG medium. Intriguingly, the majority of these recalcitrant bacteria formed colonies faster on PS or GG medium than on PT medium, which may have contributed to their successful isolation. Taken together, this study succeeded in isolating a wide variety of Dendrobium endophytic bacteria, including predominant ones using PS and GG media, and enables performance of future studies to clarify their unknown roles associated with the growth of Dendrobium plants. IMPORTANCE Dendrobium endophytic bacteria are of great interest since their functions may contribute to the protection of endangered orchids with ornamental and medicinal values. To understand and reveal the "true roles" of the endophytes, obtaining those axenic cultures is necessary even in the metagenomic era. However, no effective methods for isolating a variety of endophytic bacteria have been established. This study first demonstrated that the use of simply modified medium is quite effective and indeed allows the isolation of more than half of the predominant endophytic bacteria inhabiting Dendrobium roots. Besides, even phylogenetically novel and/or recalcitrant endophytic bacteria were successfully obtained by the same strategy. The obtained endophytic bacteria could serve as "living material" for elucidating their unprecedented functions related to the conservation of endangered orchid plants. Furthermore, the culture method used in this study may enable the isolation of various endophytic bacteria dominating not only in orchid plants but also in other useful plants.