Bacillus stamsii sp. nov., a facultatively anaerobic sugar degrader that is numerically dominant in freshwater lake sediment

Influence of Naturally Occurring Bacteria on Embryonic and Larval Development of Common Toad Tadpoles

Amphibians, as the most threatened group of vertebrates, are the focus of investigation of various agents that could affect their fitness and survival. In this context, we examined the effects of naturally occurring bacteria and their combinations on the embryonic and larval development of common toad tadpoles (Bufo bufo). One egg string that was collected from the wild was disinfected in the lab and divided into short strings, each containing 20 eggs. These strings were exposed to three different control treatments, i.e., a sterile FETAX solution, water collected from the tadpoles' native habitat, and sterilized habitat water, as well as to three different bacterial cultures isolated from habitat water (Bacillus sp., Mesobacillus sp.). We analyzed several morphometric variables (snout-vent length, total length, and weight), the energy budget by measuring body composition (proteins, carbohydrates, and lipids), and biomarker activity (acetylcholinesterase and lactate dehydrogenase). Our results indicate that the native microbial community had a negative effect on egg and tadpole development, as sterilized habitat water supported their highest development. Additionally, when grown in FETAX, pure bacterial cultures and their combinations decreased acetylcholinesterase activity but positively affected both tadpole size and energy budget. These findings suggest that bacteria can influence the larval development of common toads by modifying physiological traits. Future research should identify which microbes have beneficial or detrimental effects on amphibian development.

Gelling and reducing agents are potential carbon and energy sources in culturing of anaerobic microorganisms

The majority of microorganisms in the environment have yet to be isolated in pure cultures, and the reasons behind this phenomenon remain elusive. In this study, we investigated the possibility of the commonly used gelling agent including agar and gellan gum as a source of carbon and energy in anaerobic roll-tube cultivation from one mangrove sediment sample and two high-temperature oilfield samples. Based on growth tests and genomic evidence, anaerobic gellan degraders were retrieved from genera of Clostridium, Lacrimispora, and lineages from the rarely cultivated phylum Atribacterota. Anaerobic agarolytic microorganisms were found to be members of Bacillus and Clostridium. We also proved the role of carbon and energy sources of L-cysteine, a routine agent used to make culture media anoxic/anaerobic in both enrichment cultures and isolated strains representing Acetomicrobium, Thermodesulfovibrio, Lacrimispora, Clostridium, Bacillus, Coprothermobacter, Citrobacter, and Enterobacter. Furthermore, the isolates and enriched microbial communities utilizing L-cysteine under anaerobic conditions were mainly through L-cysteine desulfuration to pyruvate, ammonia, and sulfide. This study demonstrates that the widely used gelling and reducing agents in the basal medium can serve as carbon and energy sources for anaerobic microorganisms and thus may bias the enrichment and isolation.

IMPORTANCE

Most microbial species inhabiting natural environments have not been isolated in pure cultures using conventional media and laboratory conditions, but the reason behind this is unclear. Here, we provided a new explanation for the phenomenon, in that both the gelling agents, like agar and gellan gum, and reducing agent L-cysteine-HCl in the media provide extra carbon and energy sources to microorganisms and therefore decrease the chance in isolation specifically for the supplemented substrate which is supposed to be the sole source of carbon and energy. This result demonstrated that further improvement in the effectiveness of isolation of targeted microorganisms will be facilitated by subtracting the overlooked organic ingredients in the medium and more innovations.

Comparative Analysis of Brucepastera parasyntrophica gen. nov., sp. nov. and Teretinema zuelzerae gen. nov., comb. nov. (Treponemataceae) Reveals the Importance of Interspecies Hydrogen Transfer in the Energy Metabolism of Spirochetes

Most members of the family Treponemataceae (Spirochaetales) are associated with vertebrate hosts. However, a diverse clade of uncultured, putatively free-living treponemes comprising several genus-level lineages is present in other anoxic environments. The only cultivated representative to date is Treponema zuelzerae, isolated from freshwater mud. Here, we describe the isolation of strain RmG11 from the intestinal tract of cockroaches. The strain represents a novel genus-level lineage of Treponemataceae and is metabolically distinct from T. zuelzerae. While T. zuelzerae grows well on various sugars, forming acetate and H₂ as major fermentation products, strain RmG11 grew poorly on glucose, maltose, and starch, forming mainly ethanol and only small amounts of acetate and H₂. In contrast to the growth of T. zuelzerae, that of strain RmG11 was strongly inhibited at high H₂ partial pressures but improved considerably when H₂ was removed from the headspace. Cocultures of strain RmG11 with the H₂-consuming Methanospirillum hungatei produced acetate and methane but no ethanol. Comparative genomic analysis revealed that strain RmG11 possesses only a single, electron-confurcating hydrogenase that forms H₂ from NADH and reduced ferredoxin, whereas T. zuelzerae also possesses a second, ferredoxin-dependent hydrogenase that allows the thermodynamically more favorable formation of H₂ from ferredoxin via the Rnf complex. In addition, we found that T. zuelzerae utilizes xylan and possesses the genomic potential to degrade other plant polysaccharides. Based on phenotypic and phylogenomic evidence, we describe strain RmG11 as Brucepastera parasyntrophica gen. nov., sp. nov. and Treponema zuelzerae as Teretinema zuelzerae gen. nov., comb. nov. IMPORTANCE Spirochetes are widely distributed in various anoxic environments and commonly form molecular hydrogen as a major fermentation product. Here, we show that two closely related members of the family Treponemataceae differ strongly in their sensitivity to high hydrogen partial pressure, and we explain the metabolic mechanisms that cause these differences by comparative genome analysis. We demonstrate a strong boost in the growth of the hydrogen-sensitive strain and a shift in its fermentation products to acetate during cocultivation with a H₂-utilizing methanogen. Our results add a hitherto unrecognized facet to the fermentative metabolism of spirochetes and also underscore the importance of interspecies hydrogen transfer in not-obligately-syntrophic interactions among fermentative and hydrogenotrophic guilds in anoxic environments.

Phosphitispora fastidiosa gen. nov. sp. nov., a new dissimilatory phosphite-oxidizing anaerobic bacterium isolated from anaerobic sewage sludge

A new strictly anaerobic bacterium, strain DYL19^T, was enriched and isolated with phosphite as the sole electron donor and CO₂ as a single carbon source and electron acceptor from anaerobic sewage sludge sampled at a sewage treatment plant in Constance, Germany. It is a Gram-positive, spore-forming, slightly curved, rod-shaped bacterium which oxidizes phosphite to phosphate while reducing CO₂ to biomass and small amounts of acetate. Optimal growth is observed at 30 °C, pH 7.2, with a doubling time of 3 days. Beyond phosphite, no further inorganic or organic electron donor can be used, and no other electron acceptor than CO₂ is reduced. Sulphate inhibits growth with phosphite and CO₂. The G+C content is 45.95 mol%, and dimethylmenaquinone-7 is the only quinone detectable in the cells. On the basis of 16S rRNA gene sequence analysis and other chemotaxonomic properties, strain DYL19^T is described as the type strain of a new genus and species, Phosphitispora fastidiosa gen. nov., sp. nov.

Variability of the structure of winter microbial communities in Chelyabinsk lakes

Microorganisms form complex and dynamic communities that play a key role in the biogeochemical cycles of lakes. A high level of urbanization is currently a serious threat to bacterial communities and the ecosystem of freshwater bodies. To assess the contribution of anthropogenic load to variations in the structure of winter microbial communities in lakes, microorganisms of four water bodies of Chelyabinsk region were studied for the first time. We used cultural, chromatography-mass spectrometric, and modern methods of statistical data processing (particularly, multivariate exploratory analysis and canonical analysis of correspondences). The research showed that the composition of winter microbial communities in lakes Chebarkul’, Smolino, Pervoye, and Shershenevskoye Reservoir did not differ significantly between the main phyla of microorganisms. The dominant microorganisms were found to be of the Firmicutes phylum and Actinobacteria phylum. The structure of bacterial communities had special features depending on the characteristics of the water body and the sampling depths. Thus, in the lakes Smolino, Pervoye, and Shershenevskoye Reservoir, an important role was played by associations between microorganisms – indicators of fecal contamination: coliform bacteria and Enterococcus. On the contrary, in Chebarkul’ Lake, members of the genus Bacillus, which are natural bioremediators, formed stable winter associations. However, the differences between water bodies and sampling depths reflected 28.1% and 9.8% of the variability of the winter microbial communities, respectively. The largest contribution (about 60%) to the variability of the structure was made by intra-water processes, which determined the high heterogeneity of samples from different water areas. We assume that an important role in this variability was played by the high anthropogenic impact in a large industrial metropolis. In our opinion, this line of research is very promising for addressing key environmental issues.

Variability of the structure of winter microbial communities in Chelyabinsk lakes

Microorganisms form complex and dynamic communities that play a key role in the biogeochemical cycles of lakes. A high level of urbanization is currently a serious threat to bacterial communities and the ecosystem of freshwater bodies. To assess the contribution of anthropogenic load to variations in the structure of winter microbial communities in lakes, microorganisms of four water bodies of Chelyabinsk region were studied for the first time. We used cultural, chromatography-mass spectrometric, and modern methods of statistical data processing (particularly, multivariate exploratory analysis and canonical analysis of correspondences). The research showed that the composition of winter microbial communities in lakes Chebarkul’, Smolino, Pervoye, and Shershenevskoye Reservoir did not differ significantly between the main phyla of microorganisms. The dominant microorganisms were found to be of the Firmicutes phylum and Actinobacteria phylum. The structure of bacterial communities had special features depending on the characteristics of the water body and the sampling depths. Thus, in the lakes Smolino, Pervoye, and Shershenevskoye Reservoir, an important role was played by associations between microorganisms – indicators of fecal contamination: coliform bacteria and Enterococcus. On the contrary, in Chebarkul’ Lake, members of the genus Bacillus, which are natural bioremediators, formed stable winter associations. However, the differences between water bodies and sampling depths reflected 28.1% and 9.8% of the variability of the winter microbial communities, respectively. The largest contribution (about 60%) to the variability of the structure was made by intra-water processes, which determined the high heterogeneity of samples from different water areas. We assume that an important role in this variability was played by the high anthropogenic impact in a large industrial metropolis. In our opinion, this line of research is very promising for addressing key environmental issues.

Pelorhabdus rhamnosifermentans gen. nov., sp. nov., a strictly anaerobic rhamnose degrader from freshwater lake sediment

A rhamnose-degrading bacterium, strain BoRhaA^T, was isolated from profundal sediment of Lake Constance in agar dilution series with l-rhamnose as substrate and with a background lawn of Methanospirillum hungatei. The isolated strain was a motile rod that stained Gram positive. Growth was observed within a pH range of 4.0-7.5 and a temperature range of 15-30°C. Fermentation products of rhamnose or glucose were acetate, propionate, ethanol, butyrate, and 1-propanol. The G+C content was 40.6% G+C. The dominant fatty acids are C_16:1ω9c, i-C_13:03OH, C_16:0 and C_17:1ω8c with 8-21% relative abundance. Polar lipids were glycolipids, phosphatidylethanolamine, phosphoaminolipid and other lipids, of which phosphatidylethanolamine was most abundant. The sequence of the 16S rRNA gene of the new isolate matches the sequence of its closest relative Anaerosporomusa subterranea to 92.4%. A comparison of the genome with this strain showed 60.2% genome-wide average amino acid identity (AAI), comparisons with other type strains showed a maximum of 62.7% AAI. Thus, the definition of a new genus is justified for which we propose the name Pelorhabdus. For strain BoRhaA^T, we propose the name Pelorhabdus rhamnosifermentans gen. nov., sp. nov., with strain BoRhaA^T (DSM 111565^T = JCM 39158^T) as the type strain.

Isolation of a member of the candidate phylum 'Atribacteria' reveals a unique cell membrane structure

A key feature that differentiates prokaryotic cells from eukaryotes is the absence of an intracellular membrane surrounding the chromosomal DNA. Here, we isolate a member of the ubiquitous, yet-to-be-cultivated phylum ‘Candidatus Atribacteria’ (also known as OP9) that has an intracytoplasmic membrane apparently surrounding the nucleoid. The isolate, RT761, is a subsurface-derived anaerobic bacterium that appears to have three lipid membrane-like layers, as shown by cryo-electron tomography. Our observations are consistent with a classical gram-negative structure with an additional intracytoplasmic membrane. However, further studies are needed to provide conclusive evidence for this unique intracellular structure. The RT761 genome encodes proteins with features that might be related to the complex cellular structure, including: N-terminal extensions in proteins involved in important processes (such as cell-division protein FtsZ); one of the highest percentages of transmembrane proteins among gram-negative bacteria; and predicted Sec-secreted proteins with unique signal peptides. Physiologically, RT761 primarily produces hydrogen for electron disposal during sugar degradation, and co-cultivation with a hydrogen-scavenging methanogen improves growth. We propose RT761 as a new species, Atribacter laminatus gen. nov. sp. nov. and a new phylum, Atribacterota phy. nov.

A key feature that differentiates prokaryotic cells from eukaryotes is the absence of an intracellular membrane surrounding the chromosomal DNA. Here, the authors isolate a member of the ubiquitous, yet-to-be-cultivated bacterial phylum ‘Candidatus Atribacteria’ that has an intracytoplasmic membrane apparently surrounding the nucleoid.

Mesobacillus harenae sp. nov., isolated from the sandy soil of a cold desert

A bacterial strain, designated Y40^T, was isolated from sandy soil sampled on the Qinghai-Tibet Plateau. A polyphasic study confirmed the affiliation of the strain with the genus Mesobacillus. Strain Y40^T was found to be an aerobic, Gram-stain-positive, motile and rod-shaped bacterium. The strain grew at 10-42 °C, pH 6-9 and with 0-2 % (w/v) NaCl. The diagnostic amino acid was meso-diaminopimeilic acid. MK7 was predominant menaquinone, and iso-C_15:0, iso-C_17:1 ω10c and anteiso-C_15:0 were the major fatty acids. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified lipid. The DNA G+C content was 40.6 mol%. Based on he results of 16S rRNA gene sequence analysis, strain Y40^T was phylogenetically closely related to Mesobacillus zeae JJ-247^T and Mesobacillus foraminis CV53^T, with similarities of 98.0 and 97.7 %, respectively. The average nucleotide identity (ANIb) values between strain Y40^T and Mesobacillus zeae JJ-247^T and Mesobacillus foraminis CV53^T were 69.9 and 70.0 %, respectively. Based on the morphological, physiological, and chemotaxonomic data, it is proposed that strain Y40^T (=CICC 24459^T=JCM 32794^T) should be classified into the genus Mesobacillus as Mesobacillus harenae sp. nov.

High-efficiency methanogenesis via kitchen wastes served as ethanol source to establish direct interspecies electron transfer during anaerobic Co-digestion with waste activated sludge

Kitchen wastes (KW) have been widely investigated for bio-ethanol production, while no study utilizes KW as ethanol source to stimulate the methanogenic communities to perform direct interspecies electron transfer (DIET), since the excess acidity contained after the biological ethanol-type fermentation pretreatment (BEFP) can seriously inhibit the DIET-based syntrophic metabolism. In this study, a strategy that utilized waste activated sludge (WAS) as co-substrate to relieve the excess acidity after BEFP during anaerobic co-digestion (AcoD) was proposed. The results showed that, under the mixed ratio of 1:2 and 1:5 (KW:WAS, volume ratio), both methane production and organic compound removal evidently increased, compared with that treating the sole WAS. Conversely, under the other mixed ratios (sole KW, 5:1, 2:1 and 1:1), no methane but the evident hydrogen production was detected, and syntrophic metabolism of organic acids and alcohols was prevented. Three-dimensional excitation emission matrix (3D-EEM) analysis showed that the protein-like organic compounds contained in both KW and WAS were effectively degraded. Furthermore, the maximum methane production potential from WAS during AcoD (260.5 ± 4.1 and 264.3 ± 2.7 mL/g-COD) was higher than that treating sole WAS (250.8 ± 0.1 mL/g-COD). Microbial community analysis showed that, some genera capable of metabolizing the complex organic compounds with the reduction of the elemental sulfur or equipped with the electrically conductive pili were specially enriched during AcoD under the mixed ratio of 1:2 and 1:5. They might proceed DIET with methanogens, such as Methanosarcina and Methanospirillum species, to maintain the syntrophic metabolism effective and stable, since the abundance of both Methanosarcina and Methanospirillum species evidently increased.

A phylogenomic and comparative genomic framework for resolving the polyphyly of the genus Bacillus: Proposal for six new genera of Bacillus species, Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov

The genus Bacillus, harbouring 293 species/subspecies, constitutes a phylogenetically incoherent group. In the absence of reliable means for grouping known Bacillus species into distinct clades, restricting the placement of new species into this genus has proven difficult. To clarify the evolutionary relationships among Bacillus species, 352 available genome sequences from the family Bacillaceae were used to perform comprehensive phylogenomic and comparative genomic analyses. Four phylogenetic trees were reconstructed based on multiple datasets of proteins including 1172 core Bacillaceae proteins, 87 proteins conserved within the phylum Firmicutes, GyrA-GyrB-RpoB-RpoC proteins, and UvrD-PolA proteins. All trees exhibited nearly identical branching of Bacillus species and consistently displayed six novel monophyletic clades encompassing 5-23 Bacillus species (denoted as the Simplex, Firmus, Jeotgali, Niacini, Fastidiosus and Alcalophilus clades), interspersed with other Bacillaceae species. Species from these clades also generally grouped together in 16S rRNA gene trees. In parallel, our comparative genomic analyses of Bacillus species led to the identification of 36 molecular markers comprising conserved signature indels in protein sequences that are specifically shared by the species from these six observed clades, thus reliably demarcating these clades based on multiple molecular synapomorphies. Based on the strong evidence from multiple lines of investigations supporting the existence of these six distinct 'Bacillus' clades, we propose the transfer of species from these clades into six novel Bacillaceae genera viz. Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov. These results represent an important step towards clarifying the phylogeny/taxonomy of the genus Bacillus.