Isolation and characterization of Desulfocurvus thunnarius sp. nov., a sulfate-reducing bacterium isolated from an anaerobic sequencing batch reactor treating cooking wastewater

Establishment of Genome Based Criteria for Classification of the Family Desulfovibrionaceae and Proposal of Two Novel Genera, Alkalidesulfovibrio gen. nov. and Salidesulfovibrio gen. nov

Bacteria in the Desulfovibrionaceae family, which contribute to S element turnover as sulfate-reducing bacteria (SRB) and disproportionation of partially oxidized sulfoxy anions, have been extensively investigated since the importance of the sulfur cycle emerged. Novel species belonging to this taxon are frequently reported, because they exist in various environments and are easy to culture using established methods. Due to the rapid expansion of the taxon, correction and reclassification have been conducted. The development of high-throughput sequencing facilitated rapid expansion of genome sequence database. Genome-based criteria, based on these databases, proved to be potential classification standard by overcoming the limitations of 16S rRNA-based phylogeny. Although standards methods for taxogenomics are being established, the addition of a novel genus requires extensive calculations with taxa, including many species, such as Desulfovibrionaceae. Thus, the genome-based criteria for classification of Desulfovibrionaceae were established and validated in this study. The average amino-acid identity (AAI) cut-off value, 63.43 ± 0.01, was calculated to be an appropriate criterion for genus delineation of the family Desulfovibrionaceae. By applying the AAI cut-off value, 88 genomes of the Desulfovibrionaceae were divided into 27 genera, which follows the core gene phylogeny results. In this process, two novel genera (Alkalidesulfovibrio and Salidesulfovibrio) and one former invalid genus (“Psychrodesulfovibrio”) were officially proposed. Further, by applying the 95–96% average nucleotide identity (ANI) standard and the 70% digital DNA–DNA hybridization standard values for species delineation of strains that were classified as the same species, five strains have the potential to be newly classified. After verifying that the classification was appropriately performed through relative synonymous codon usage analysis, common characteristics were listed by group. In addition, by detecting metal resistance related genes via in silico analysis, it was confirmed that most strains display metal tolerance.

Resistance and Resilience of Sulfidogenic Communities in the Face of the Specific Inhibitor Perchlorate

Hydrogen sulfide is a toxic and corrosive gas, produced by the activity of sulfate-reducing microorganisms (SRM). Owing to the environmental, economic and human-health consequences of sulfide, there is interest in developing specific inhibitors of SRM. Recent studies have identified perchlorate as a promising emerging inhibitor. The aim of this work is to quantitatively dissect the inhibitory dynamics of perchlorate. Sulfidogenic mixed continuous-flow systems were treated with perchlorate. SRM number, sulfide production and community structure were monitored pre-, during and post-treatment. The data generated was compared to a simple mathematical model, where SRM growth slows as a result of inhibition. The experimental data supports the interpretation that perchlorate largely acts to suppress SRM growth rates, rendering planktonic SRM increasingly susceptible to wash-out. Surface-attachment was identified as an important parameter preventing SRM wash-out and thus governing inhibitory dynamics. Our study confirmed the lesser depletion of surface-attached SRM as compared to planktonic SRM during perchlorate treatment. Indirect effects of perchlorate (bio-competitive exclusion of SRM by dissimilatory perchlorate-reducing bacteria, DPRB) were also assayed by amending reactors with DPRB. Indeed, low concentrations of perchlorate coupled with DRPB amendment can drive sulfide concentrations to zero. Further, inhibition in a complex community was compared to that in a pure culture, highlighting similarities and differences between the two scenarios. Finally, we quantified susceptibility to perchlorate across SRM in various culture conditions, showing that prediction of complex behavior in continuous systems from batch results is possible. This study thus provides an overview of the sensitivity of sulfidogenic communities to perchlorate, as well as mechanisms underlying these patterns.

Pseudodesulfovibrio indicus gen. nov., sp. nov., a piezophilic sulfate-reducing bacterium from the Indian Ocean and reclassification of four species of the genus Desulfovibrio

A novel sulfate-reducing bacterium, strain J2T, was isolated from a serpentinized peridotite sample from the Indian Ocean. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain J2T clustered with the genus Desulfovibrio within the family Desulfovibrionaceae, but it showed low similarity (87.95 %) to the type species Desulfovibrio desulfuricans DSM 642T. It was most closely related to Desulfovibrio portus MSL79T (96.96 %), followed by Desulfovibrio aespoeensis Aspo-2T (96.11 %), Desulfovibrio piezophilus C1TLV30T (96.04 %) and Desulfovibrio profundus DSM 11384T (95.17 %). Other available sequences shared less than 93.33 % 16S rRNA gene sequence similarity. Cells were Gram-staining-negative, anaerobic, motile vibrios (2-6×0.4-0.6 µm). Growth was observed at salinities ranging from 0.2 to 6 % (optimum 2.5 %), from pH 5 to 8 (optimum pH 6.5-7) and at temperatures between 9 and 40 °C (optimum 30-35 °C). J2T was piezophilic, growing optimally at 10 MPa (range 0-30 MPa). J2T used lactate, malate, pyruvate, formate and hydrogen as energy sources. Sulfate, thiosulfate, sulfite, fumarate and nitrate were used as terminal electron acceptors. Lactate and pyruvate were fermented. The main fatty acids were iso-C15 : 0, anteiso-C15 : 0, summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl) and iso-C17 : 0. The DNA G+C content of strain J2T was 63.5 mol%. The combined genotypic and phenotypic data show that strain J2T represents a novel species of a novel genus in the family Desulfovibrionaceae, for which the name Pseudodesulfovibrio indicus gen. nov., sp. nov. is proposed, with the type strain J2T (=MCCC 1A01867T = DSM 101483T). We also propose the reclassification of D. piezophilus as Pseudodesulfovibrio piezophilus comb. nov., D. profundus as Pseudodesulfovibrio profundus comb. nov., D. portus as Pseudodesulfovibrio portus comb. nov. and D. aespoeensis as Pseudodesulfovibrio aespoeensis comb. nov.

High-throughput Methods Redefine the Rumen Microbiome and Its Relationship with Nutrition and Metabolism

Diversity in the forestomach microbiome is one of the key features of ruminant animals. The diverse microbial community adapts to a wide array of dietary feedstuffs and management strategies. Understanding rumen microbiome composition, adaptation, and function has global implications ranging from climatology to applied animal production. Classical knowledge of rumen microbiology was based on anaerobic, culture-dependent methods. Next-generation sequencing and other molecular techniques have uncovered novel features of the rumen microbiome. For instance, pyrosequencing of the 16S ribosomal RNA gene has revealed the taxonomic identity of bacteria and archaea to the genus level, and when complemented with barcoding adds multiple samples to a single run. Whole genome shotgun sequencing generates true metagenomic sequences to predict the functional capability of a microbiome, and can also be used to construct genomes of isolated organisms. Integration of high-throughput data describing the rumen microbiome with classic fermentation and animal performance parameters has produced meaningful advances and opened additional areas for study. In this review, we highlight recent studies of the rumen microbiome in the context of cattle production focusing on nutrition, rumen development, animal efficiency, and microbial function.