Sphaerochaeta halotolerans sp. nov., a novel spherical halotolerant spirochete from a Russian heavy oil reservoir, emended description of the genus Sphaerochaeta, reclassification of Sphaerochaeta coccoides to a new genus Parasphaerochaeta gen. nov. as Parasphaerochaeta coccoides comb. nov. and proposal of Sphaerochaetaceae fam. nov

Anaerobic membrane bioreactor (AnMBR) with external ultrafiltration membrane for the treatment of sugar beet vinasse

Vinasse, a by-product of ethanol production, is generated at significant rates. While rich in nutrients such as calcium, magnesium, and potassium, its high solids, organic matter, acidity, and sulfate content pose challenges when disposed directly on soil, necessitating treatment. Anaerobic digestion is a viable solution, reducing organic pollution while recovering energy in the form of biogas, aligning with the biorefinery concept. Traditionally, sludge bed reactors and anaerobic contact reactors are utilized for vinasse processing, with sludge granulation being vital for treatment success. However, challenges such as sludge wash-out due to recalcitrant compounds, high solids concentration in the influent, low pH, salinity, and temperature hinder granule formation. Anaerobic membrane bioreactors (AnMBR) offer an alternative, simplifying treatment by integrating intensified pre- and post-treatment units. Due to complete sludge retention, AnMBRs achieve high COD removal efficiencies, yielding a suspended solids-free and largely disinfected effluent. Therefore, AnMBRs show promise for vinasse treatment, eliminating the need for sludge granulation and producing nutrient-rich effluent with minimal residual organics and suspended solids. In this study, an AnMBR equipped with an inside-out external crossflow ultrafiltration membrane was proposed for the treatment of vinasse. The AnMBR reached a COD removal efficiency of 95% ± 2.6% and produced 0.3 CH4 L. g COD removed -1 working at organic loading rates of 8 g COD. L-1 d-1 and membrane fluxes of 10 LMH. At organic loading rates of 10 g COD. L-1 d-1 and fluxes of 12 and 14 LMH, the COD removal efficiency decreased to 77% ± 11% and 73% ± 7.9%, respectively. The AnMBR technology represents an innovation for wastewater treatment, however, more research using the cross-flow configuration and different types of effluents is needed. Literature studies that address the treatment of sugar beet or sugarcane vinasse using AnMBR are still scarce. This study explored the potentials of AnMBR technology for vinasse treatment and contributes to the dissemination of this technology, opening new possibilities for vinasse processing.

Phenotypic and Genomic Characterization of a Sulfate-Reducing Bacterium Pseudodesulfovibrio methanolicus sp. nov. Isolated from a Petroleum Reservoir in Russia

The search for the microorganisms responsible for sulfide formation and corrosion of steel equipment in the oil fields of Tatarstan (Russia) resulted in the isolation of a new halotolerant strictly anaerobic sulfate-reducing bacterium, strain 5S69T. The cells were motile curved Gram-negative rods. Optimal growth was observed in the presence of 2.0-4.0% (w/v) NaCl, at pH 6.5, and at 23-28 °C under sulfate-reducing conditions. The isolate was capable of chemoorganotrophic growth with sulfate and other sulfoxides as electron acceptors, resulting in sulfide formation; and of pyruvate fermentation resulting in formation of H2 and acetate. The strain utilized lactate, pyruvate, ethanol, methanol, fumarate, and fructose, as well as H2/CO2/acetate for sulfate reduction. The genome size of the type strain 5S69T was 4.16 Mb with a G + C content of 63.0 mol%. On the basis of unique physiological properties and results of the 16S rRNA gene-based phylogenetic analysis, phylogenomic analysis of the 120 conserved single copy proteins and genomic indexes (ANI, AAI, and dDDH), assigning the type strain 5S69T ((VKM B-3653T = KCTC 25499T) to a new species within the genus Pseudodesulfovibrio, is suggested, with the proposed name Pseudodesulfovibrio methanolicus sp. nov. Genome analysis of the new isolate showed several genes involved in sulfate reduction and its sulfide-producing potential in oil fields with high saline formation water.

Phylogenomic analysis of metagenome-assembled genomes indicates new taxa in the order Spirochaetales and proposal of Thalassospirochaeta sargassi gen. nov. sp. nov. from seaweeds

Six metagenome-assembled genomes (JB008Ts, JB007, JB015, JB003, JB004, and JB002) belonging to the order Spirochaetales were generated from seaweed samples collected from the Gulf of Mannar, India. The binned genomes JB008Ts and JB007 shared highest 16S rRNA gene identity of 94.9 % and 92.2-93.4 %, respectively with uncultivated Spirochaetaceae family members, and < 90 % identity with Marispirochaeta aestuari JC444T. While, the bin JB015 showed 99.1 % identity with Pleomorphochaeta naphthae SEBR 4209T. The phylogenomic and 16S rRNA gene-based phylogenetic analysis of the binned genomes JB007 and JB008Ts confirmed that these members belong to the family Spirochaetaceae and bins JB015, JB002, JB003, and JB004 belong to the genus Pleomorphochaeta within the family Sphaerochaetaceae. The AAI values of the binned genomes JB007 and JB008Ts compared to other members of the Spirochaetaceae family were between 53.9- 56.8 % and 53.8-57.1 %, respectively. Furthermore, the comparison of ANI, dDDH, and POCP metrics of the binned genomes JB007 and JB008Ts, both among themselves and with the members of Spirochaetaceae, was also below the suggested thresholds for genera delineation. Consequently, the binned genome JB008Ts is proposed as a new genus according to the guidelines of code of nomenclature of prokaryotes described from sequence data (SeqCode) with the name Thalassospirochaeta sargassi gen. nov. sp. nov., in the family Spirochaetaceae while the bin JB007 could not be proposed as novel taxa due to low-quality estimates. The bin JB015 and its additional genomes form a distinct clade, but their taxonomic status remains ambiguous due to the absence of genomic evidence from other Pleomorphochaeta members.

Metagenomic and Culture-Based Analyses of Microbial Communities from Petroleum Reservoirs with High-Salinity Formation Water, and Their Biotechnological Potential

The reserves of light conditional oil in reservoirs with low-salinity formation water are decreasing worldwide, necessitating the extraction of heavy oil from petroleum reservoirs with high-salinity formation water. As the first stage of defining the microbial-enhanced oil recovery (MEOR) strategies for depleted petroleum reservoirs, microbial community composition was studied for petroleum reservoirs with high-salinity formation water located in Tatarstan (Russia) using metagenomic and culture-based approaches. Bacteria of the phyla Desulfobacterota, Halanaerobiaeota, Sinergistota, Pseudomonadota, and Bacillota were revealed using 16S rRNA-based high-throughput sequencing in halophilic microbial communities. Sulfidogenic bacteria predominated in the studied oil fields. The 75 metagenome-assembled genomes (MAGs) of prokaryotes reconstructed from water samples were assigned to 16 bacterial phyla, including Desulfobacterota, Bacillota, Pseudomonadota, Thermotogota, Actinobacteriota, Spirochaetota, and Patescibacteria, and to archaea of the phylum Halobacteriota (genus Methanohalophilus). Results of metagenomic analyses were supported by the isolation of 20 pure cultures of the genera Desulfoplanes, Halanaerobium, Geotoga, Sphaerochaeta, Tangfeifania, and Bacillus. The isolated halophilic fermentative bacteria produced oil-displacing metabolites (lower fatty acids, alcohols, and gases) from sugar-containing and proteinaceous substrates, which testify their potential for MEOR. However, organic substrates stimulated the growth of sulfidogenic bacteria, in addition to fermenters. Methods for enhanced oil recovery should therefore be developed, combining the production of oil-displacing compounds with fermentative bacteria and the suppression of sulfidogenesis.

Genome Analysis and Potential Ecological Functions of Members of the Genus Ensifer from Subsurface Environments and Description of Ensifer oleiphilus sp. nov

The current work deals with genomic analysis, possible ecological functions, and biotechnological potential of two bacterial strains, HO-A22T and SHC 2-14, isolated from unique subsurface environments, the Cheremukhovskoe oil field (Tatarstan, Russia) and nitrate- and radionuclide-contaminated groundwater (Tomsk region, Russia), respectively. New isolates were characterized using polyphasic taxonomy approaches and genomic analysis. The genomes of the strains HO-A22T and SHC 2-14 contain the genes involved in nitrate reduction, hydrocarbon degradation, extracellular polysaccharide synthesis, and heavy metal detoxification, confirming the potential for their application in various environmental biotechnologies. Genomic data were confirmed by cultivation studies. Both strains were found to be neutrophilic, chemoorganotrophic, facultatively anaerobic bacteria, growing at 15-33 °C and 0-1.6% NaCl (w/v). The 16S rRNA gene sequences of the strains were similar to those of the type strains of the genus Ensifer (99.0-100.0%). Nevertheless, genomic characteristics of strain HO-A22T were below the thresholds for species delineation: the calculated average nucleotide identity (ANI) values were 83.7-92.4% (<95%), and digital DNA-DNA hybridization (dDDH) values were within the range of 25.4-45.9% (<70%), which supported our conclusion that HO-A22T (=VKM B-3646T = KCTC 92427T) represented a novel species of the genus Ensifer, with the proposed name Ensifer oleiphilus sp. nov. Strain SHC 2-14 was assigned to the species 'Ensifer canadensis', which has not been validly published. This study expanded the knowledge about the phenotypic diversity among members of the genus Ensifer and its potential for the biotechnologies of oil recovery and radionuclide pollution treatment.

A Variant of the Sulfoglycolytic Transketolase Pathway for the Degradation of Sulfoquinovose into Sulfoacetate

Sulfoquinovose (SQ, 6-deoxy-6-sulfo-glucose) constitutes the polar head group of plant sulfolipids and is one of the most abundantly produced organosulfur compounds in nature. Degradation of SQ by bacterial communities contributes to sulfur recycling in many environments. Bacteria have evolved at least four mechanisms for glycolytic degradation of SQ, termed sulfoglycolysis, producing C3 sulfonate (dihydroxypropanesulfonate and sulfolactate) and C2 sulfonate (isethionate) by-products. These sulfonates are further degraded by other bacteria, leading to the mineralization of the sulfonate sulfur. The C2 sulfonate sulfoacetate is widespread in the environment and is also thought to be a product of sulfoglycolysis, although the mechanistic details are yet unknown. Here, we describe a gene cluster in an Acholeplasma sp., from a metagenome derived from deeply circulating subsurface aquifer fluids (GenBank accession no. QZKD01000037), encoding a variant of the recently discovered sulfoglycolytic transketolase (sulfo-TK) pathway that produces sulfoacetate instead of isethionate as a by-product. We report the biochemical characterization of a coenzyme A (CoA)-acylating sulfoacetaldehyde dehydrogenase (SqwD) and an ADP-forming sulfoacetate-CoA ligase (SqwKL), which collectively catalyze the oxidation of the transketolase product sulfoacetaldehyde into sulfoacetate, coupled with ATP formation. A bioinformatics study revealed the presence of this sulfo-TK variant in phylogenetically diverse bacteria, adding to the variety of mechanisms by which bacteria metabolize this ubiquitous sulfo-sugar. IMPORTANCE Many bacteria utilize environmentally widespread C2 sulfonate sulfoacetate as a sulfur source, and the disease-linked human gut sulfate- and sulfite-reducing bacteria can use it as a terminal electron receptor for anaerobic respiration generating toxic H2S. However, the mechanism of sulfoacetate formation is unknown, although it has been proposed that sulfoacetate originates from bacterial degradation of sulfoquinovose (SQ), the polar head group of sulfolipids present in all green plants. Here, we describe a variant of the recently discovered sulfoglycolytic transketolase (sulfo-TK) pathway. Unlike the regular sulfo-TK pathway that produces isethionate, our biochemical assays with recombinant proteins demonstrated that a CoA-acylating sulfoacetaldehyde dehydrogenase (SqwD) and an ADP-forming sulfoacetate-CoA ligase (SqwKL) in this variant pathway collectively catalyze the oxidation of the transketolase product sulfoacetaldehyde into sulfoacetate, coupled with ATP formation. A bioinformatics study revealed the presence of this sulfo-TK variant in phylogenetically diverse bacteria and interpreted the widespread existence of sulfoacetate.

A metagenome-level analysis of a microbial community fermenting ultra-filtered milk permeate

Fermentative microbial communities have the potential to serve as biocatalysts for the conversion of low-value dairy coproducts into renewable chemicals, contributing to a more sustainable global economy. To develop predictive tools for the design and operation of industrially relevant strategies that utilize fermentative microbial communities, there is a need to determine the genomic features of community members that are characteristic to the accumulation of different products. To address this knowledge gap, we performed a 282-day bioreactor experiment with a microbial community that was fed ultra-filtered milk permeate, a low-value coproduct from the dairy industry. The bioreactor was inoculated with a microbial community from an acid-phase digester. A metagenomic analysis was used to assess microbial community dynamics, construct metagenome-assembled genomes (MAGs), and evaluate the potential for lactose utilization and fermentation product synthesis of community members represented by the assembled MAGs. This analysis led us to propose that, in this reactor, members of the Actinobacteriota phylum are important in the degradation of lactose, via the Leloir pathway and the bifid shunt, and the production of acetic, lactic, and succinic acids. In addition, members of the Firmicutes phylum contribute to the chain-elongation-mediated production of butyric, hexanoic, and octanoic acids, with different microbes using either lactose, ethanol, or lactic acid as the growth substrate. We conclude that genes encoding carbohydrate utilization pathways, and genes encoding lactic acid transport into the cell, electron confurcating lactate dehydrogenase, and its associated electron transfer flavoproteins, are genomic features whose presence in Firmicutes needs to be established to infer the growth substrate used for chain elongation.

Effects of fermented Andrographis paniculata on growth performance, carcass traits, immune function, and intestinal health in Muscovy ducks

The study aimed to examine the effects of unfermented and fermented Andrographis paniculata on growth performance, carcass traits, immune function, and intestinal health in Muscovy ducks. A total of 450 (16-day-old) Muscovy ducks weighing 271.44 ± 8.25 g were randomly assigned to 5 dietary treatments (6 replicate pens of 15 ducks per treatment), consisting of one control treatment (basal diet without A. paniculata), one unfermented A. paniculata treatment (basal diet plus 30 g/kg unfermented A. paniculata) and 3 fermented A. paniculata treatments (basal diet plus 10, 30, and 50 g/kg). 30 g/kg unfermented A. paniculata increased the ADG, thymus index, peripheral blood lymphocyte conversion rate, villi height, intestinal thickness, villi surface area, intraepithelial lymphocytes rate, while decreased the FCR. 10 g/kg fermented A. paniculata markedly boosted ADG, bursa of fabricius index, thymus index, serum lysozyme, lymphocyte conversion rate, villi height, vilii width, intestinal thickness, villi surface area, while decreased the FCR. 30 g/kg fermented A. paniculata clearly improved ADG, bursa of fabricius index, thymus index, serum lysozyme, lymphocyte conversion rate, villi height, vilii width, intestinal thickness, villi surface area, intraepithelial lymphocytes, while decreased FCR. 50 g/kg fermented A. paniculata significantly increased villi height, vilii width, and villi surface area, while clearly reduced BW. Additionally, compared to 30 g/kg unfermented A. paniculata, 30 g/kg fermented A. paniculata obviously increased bursa of fabricius indices, lymphocyte conversion rate, vilii width, villi surface area. On top of that, supplementation with unfermented and fermented A. paniculata (30 g/kg each) decreased the relative abundance of harmful bacteria (Succinivibrio, Succinatimonas, Sphaerochaeta, and Mucispirillum) and increase the abundance of beneficial bacteria (Rikenellaceae, Methanocorpusculum, Fournierella, Ruminococcaceae) in the ceca of the ducks. However, fermented A. paniculata had considerable better effects than unfermented A. paniculate on all above measured indices. Overall, these results revealed that supplementation with unfermented and fermented A. paniculata across different treatments improved growth, immune status, intestinal morphology, and intestinal microbiota composition and structure in Muscovy ducks, making it a potential alternative to antibiotics in poultry production.

Effects of fulvic acid on growth performance, serum index, gut microbiota, and metabolites of Xianju yellow chicken

Fulvic acid (FA) is a mixture of polyphenolic acid compounds extracted from humus, peat, lignite, and aquatic environments; it is used in traditional medicine to treat digestive tract diseases. The purpose of the present study was to investigate the effect of FA on growth performance, inflammation, intestinal microbiota, and metabolites in Xianju yellow chicken. The 240 Xianju yellow chickens (age, 524 days) included were randomly categorized into 4 treatments with 6 replicates per treatment and 10 birds per replicate. Birds received a basal diet or a diet supplemented with 500, 1,000, or 1,500 mg/kg of FA, for a period of 42 days. Dietary supplementation of FA improved average daily gain (ADG) and feed conversion ratio (FCR) (P > 0.05). Compared with the control group, the serum level of TNF-α in birds supplemented with FA was significantly decreased (P < 0.05), and that of IL-2 was significantly increased after administration of 1,500 mg/kg FA (P < 0.05). Analysis of gut microbiota indicated that FA reduced the relative abundance of genus Mucispirillum, Anaerofustis, and Campylobacter, but enriched genus Lachnoclostridium, Subdoligranulum, Sphaerochaeta, Oscillibacter, and Catenibacillus among others. Untargeted metabolomic analyses revealed that FA increased 7-sulfocholic acid, but reduced the levels of Taurochenodeoxycholate-7-sulfate, LysoPC 20:4 (8Z, 11Z, 14Z, 17Z), LysoPC 18:2, Phosphocholine and other 13 metabolites in the cecum. The results demonstrated that FA may potentially have a significant positive effect on the growth performance and immune function of Xianju yellow chicken through the modulation of the gut microbiota.

Physiological and Genomic Characterization of Actinotalea subterranea sp. nov. from Oil-Degrading Methanogenic Enrichment and Reclassification of the Family Actinotaleaceae

The goal of the present work was to determine the diversity of prokaryotes involved in anaerobic oil degradation in oil fields. The composition of the anaerobic oil-degrading methanogenic enrichment obtained from an oil reservoir was determined by 16S rRNA-based survey, and the facultatively anaerobic chemoorganotrophic bacterial strain HO-Ch2^T was isolated and studied using polyphasic taxonomy approach and genome sequencing. The strain HO-Ch2^T grew optimally at 28 °C, pH 8.0, and 1–2% (w/v) NaCl. The 16S rRNA gene sequence of the strain HO-Ch2^T had 98.8% similarity with the sequence of Actinotalea ferrariae CF5-4^T. The genomic DNA G + C content of strain HO-Ch2^T was 73.4%. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between the genome of strain HO-Ch2^T and Actinotalea genomes were 79.8–82.0% and 20.5–22.2%, respectively, i.e., below the thresholds for species delineation. Based on the phylogenomic, phenotypic, and chemotaxonomic characterization, we propose strain HO-Ch2^T (= VKM Ac-2850^T = KCTC 49656^T) as the type strain of a new species within the genus Actinotalea, with the name Actinotalea subterranea sp. nov. Based on the phylogenomic analysis of 187 genomes of Actinobacteria we propose the taxonomic revision of the genera Actinotalea and Pseudactinotalea and of the family Actinotaleaceae. We also propose the reclassification of Cellulomonas carbonis as Actinotalea carbonis comb. nov., Cellulomonas bogoriensis as Actinotalea bogoriensis comb. nov., Actinotalea caeni as Pseudactinotalea caeni comb. nov., and the transfer of the genus Pseudactinotalea to the family Ruaniaceae of the order Ruaniales.

Soehngenia longivitae sp. nov., a Fermenting Bacterium Isolated from a Petroleum Reservoir in Azerbaijan, and Emended Description of the Genus Soehngenia

A methanogenic enrichment growing on a medium with methanol was obtained from a petroleum reservoir (Republic of Azerbaijan) and stored for 33 years without transfers to fresh medium. High-throughput sequencing of the V4 region of the 16S rRNA gene revealed members of the genera Desulfovibrio, Soehngenia, Thermovirga, Petrimonas, Methanosarcina, and Methanomethylovorans. A novel gram-positive, rod-shaped, anaerobic fermentative bacterium, strain 1933PT, was isolated from this enrichment and characterized. The strain grew at 13-55 °C (optimum 35 °C), with 0-3.0% (w/v) NaCl (optimum 0-2.0%) and in the pH range of 6.7-8.0 (optimum pH 7.0). The 16S rRNA gene sequence similarity, the average nucleotide identity (ANI) and in silico DNA-DNA hybridization (dDDH) values between strain 1933PT and the type strain of the most closely related species Soehngenia saccharolytica DSM 12858T were 98.5%, 70.5%, and 22.6%, respectively, and were below the threshold accepted for species demarcation. Genome-based phylogenomic analysis and physiological and biochemical characterization of the strain 1933PT (VKM B-3382T = KCTC 15984T) confirmed its affiliation to a novel species of the genus Soehngenia, for which the name Soehngenia longivitae sp. nov. is proposed. Genome analysis suggests that the new strain has potential in the degradation of proteinaceous components.