Polycladospora coralii gen. nov., sp. nov., a novel member of the family Thermoactinomycetaceae isolated from stony coral in the South China Sea

Two novel filamentous bacteria, designated as IB182353T and IB182357, were isolated from stony coral of the South China Sea. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains IB182353T and IB182357 were closely related to Hazenella coriacea DSM 45707T (with 93.4 and 93.5% similarity, respectively). The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization results showed that the pairwise similarities between isolate IB182353T and the other recognized Thermoactinomycetaceae species were less than 68.9, 60.5 and 21.1 %, respectively. Both strains produced aerial and substrate mycelia, grew optimally at 25-30 °C, pH 8.0-9.0 and with 2-3 % (w/v) NaCl. The cell-wall peptidoglycan type was meso-DAP and the whole-cell hydrolysates contained ribose. The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified aminophospholipid and three unidentified phospholipids. The genomic DNA G+C content was 39.5 mol%. Strain IB182353T was distinguishable from its related type strains by the contents of two fatty acids, iso-C15 : 0 and iso-C17 : 1  ω10c. Based on polyphasic taxonomic characterization, we propose that strains IB182353T and IB182357 represent a novel genus and species within the family Thermoactinomycetaceae, for which the name Polycladospora coralii gen. nov. sp. nov. is proposed. The type strain is IB182353T (=MCCC 1K04631T=JCM 34206T).

Hyperthermophilic pretreatment composting can reduce ammonia emissions by controlling proteolytic bacterial community and the physicochemical properties

Proteolysis is the rate-limiting step in the mineralization of organic nitrogen into ammonium (NH4+) and thereby the ammonia (NH3) released during the composting. However, the dynamics of bacterial proteolytic communities related to NH3 emissions during the composting systems are mostly unknown. This study aimed to examine and compare the effects of hyperthermophilic pretreatment composting (HPC) and traditional composting (TC) methods on (i) the difference of NH3 loss and nitrogenous compounds; (ii) the dynamics of the proteolytic bacterial community involved in the proteolysis and (iii) the correlation between the proteolytic bacterial community, biophysiochemical characteristics and NH3 loss. Results revealed that the HPC decreased NH3 loss by 42% as compared to TC during 60-day composting period. This was accompanied with an inhibitory effect on protease activity in the HPC where the relative abundances of the proteolytic bacteria (Bacillus megaterium and Staphylococcus cohnii) were reduced significantly as compared to TC. Partial least-squares path modeling suggested that various physicochemical properties such as higher temperature as well as lower C/N ratio during composting played a dominant role in affecting the abundance of proteolytic bacteria, which may have been an important factor contributing to the lower NH3 loss in HPC. All these findings lead us to conclude that the HPC can significantly reduce NH3 loss by inhibiting the proteolytic bacteria and protease activity responsible for NH3 release.

Effect of oxygen deficiency on organic matter decomposition during the early stage of composting

This study aimed to elucidate the recovery of organic matter decomposition after oxygen deficiency in the early stage was replaced by aerobic conditions during composting. Oxygen deficiency at the early stage was created by supplying nitrogen gas into the composting for 3 days (LN3dA) and 5 days (LN5dA). Subsequently, air was introduced until the end of composting instead of nitrogen gas. Runs LN3dA and LN5dA had lower organic matter decomposition by 10% and 19%, respectively, compared with fully aerobic composting (LA) after oxygen deficiency was changed to aerobic conditions. Compared with fully aerobic composting, composting with oxygen deficiency at the early thermophilic stage had a different bacterial community, as analyzed by high-throughput sequencing. During vigorous organic matter decomposition, Bacillus was dominant in Run LA, whereas Caldibacillus proliferated in Runs LN3dA and LN5dA. Bacillus thermoamylovorans, Bacillus arbutinivorans, and Bacillus kokeshiiformis were hypothesized to be inhibited by Caldibacillus. Moreover, dissimilarity analysis indicated that different bacterial communities remained until the end of composting, which could be a reason for the incomplete recovery of organic matter decomposition. As analyzed by the API-ZYM kit, the enzymatic activities were also different between all composting runs. One of the characterized enzymes, α-galactosidase, displayed low activity during oxygen deficiency and could not achieve high activity with sufficient oxygen until composting was completed. Overall, our study showed that oxygen deficiency at the early thermophilic stage caused incomplete recovery of organic matter decomposition.

Bacillales: From Taxonomy to Biotechnological and Industrial Perspectives

For a long time, the genus Bacillus has been known and considered among the most applicable genera in several fields. Recent taxonomical developments resulted in the identification of more species in Bacillus-related genera, particularly in the order Bacillales (earlier heterotypic synonym: Caryophanales), with potential application for biotechnological and industrial purposes such as biofuels, bioactive agents, biopolymers, and enzymes. Therefore, a thorough understanding of the taxonomy, growth requirements and physiology, genomics, and metabolic pathways in the highly diverse bacterial order, Bacillales, will facilitate a more robust designing and sustainable production of strain lines relevant to a circular economy. This paper is focused principally on less-known genera and their potential in the order Bacillales for promising applications in the industry and addresses the taxonomical complexities of this order. Moreover, it emphasizes the biotechnological usage of some engineered strains of the order Bacillales. The elucidation of novel taxa, their metabolic pathways, and growth conditions would make it possible to drive industrial processes toward an upgraded functionality based on the microbial nature.

Distribution and preservation of the components of the engulfment. What is beyond representative genomes?

Engulfment requires the coordinated, targeted synthesis and degradation of peptidoglycan at the leading edge of the engulfing membrane to allow the mother cell to completely engulf the forespore. Proteins such as the DMP and Q:AH complexes in Bacillus subtilis are essential for engulfment, as are a set of accessory proteins including GerM and SpoIIB, among others. Experimental and bioinformatic studies of these proteins in bacteria distinct from Bacillus subtilis indicate that fundamental differences exist regarding the organization and mechanisms used to successfully perform engulfment. As a consequence, the distribution and prevalence of the proteins involved in engulfment and other proteins that participate in different sporulation stages have been studied using bioinformatic approaches. These works are based on the prediction of orthologs in the genomes of representative Firmicutes and have been helpful in tracing hypotheses about the origin and evolution of sporulation genes, some of which have been postulated as sporulation signatures. To date, an extensive study of these signatures outside of the representative Firmicutes is not available. Here, we asked whether phyletic profiles of proteins involved in engulfment can be used as signatures able to describe the sporulation phenotype. We tested this hypothesis in a set of 954 Firmicutes, finding preserved phyletic profiles defining signatures at the genus level. Finally, a phylogenetic reconstruction based on non-redundant phyletic profiles at the family level shows the non-monophyletic origin of these proteins due to gain/loss events along the phylum Firmicutes.

Co-selection of antibiotic-resistant bacteria in a paddy soil exposed to As(III) contamination with an emphasis on potential pathogens

The increased acquisition of antibiotic resistance by pathogens is a global health concern. The environmental selection of antibiotic resistance can be caused by either antibiotic residues or co-selecting agents such as toxic metal(loid)s. This study explored the potential role of As(III) as a co-selecting driver in the spread of antibiotic resistance in paddy soils. By applying high-throughput sequencing, we found that the diversity and composition of soil microbial communities was significantly altered by As(III) exposure, resulting in an increased proportion of potential pathogens (9.9%) compared to the control soil (0.1%). Meanwhile, a total of 46 As(III)-resistant isolates were obtained from As(III)-exposure soil, among which potential pathogens accounted for 54.3%. These As(III)-resistant bacteria showed a high incidence of resistance to sulfanilamide (100%) and streptomycin (88-93%). The association between antibiotic and As(III) resistances was further investigated in a potentially pathogenic isolate by whole-genome sequencing and a transcription assay. The results showed that As(III) and antibiotic resistance genes might co-occur in a mobile genomic island and be co-regulated by As(III), implying that antibiotic resistance could be co-selected by As(III) via co-resistance and co-regulation mechanisms. Overall, these results suggest that As(III) exposure provides a strong selective pressure for the expansion of soil bacterial resistome.

Multidisciplinary involvement and potential of thermophiles

The full biotechnological exploitation of thermostable enzymes in industrial processes is necessary for their commercial interest and industrious value. The heat-tolerant and heat-resistant enzymes are a key for efficient and cost-effective translation of substrates into useful products for commercial applications. The thermophilic, hyperthermophilic, and microorganisms adapted to extreme temperatures (i.e., low-temperature lovers or psychrophiles) are a rich source of thermostable enzymes with broad-ranging thermal properties, which have structural and functional stability to underpin a variety of technologies. These enzymes are under scrutiny for their great biotechnological potential. Temperature is one of the most critical parameters that shape microorganisms and their biomolecules for stability under harsh environmental conditions. This review describes in detail the sources of thermophiles and thermostable enzymes from prokaryotes and eukaryotes (microbial cell factories). Furthermore, the review critically examines perspectives to improve modern biocatalysts, its production and performance aiming to increase their value for biotechnology through higher standards, specificity, resistance, lowing costs, etc. These thermostable and thermally adapted extremophilic enzymes have been used in a wide range of industries that span all six enzyme classes. Thus, in particular, target of this review paper is to show the possibility of both high-value-low-volume (e.g., fine-chemical synthesis) and low-value-high-volume by-products (e.g., fuels) by minimizing changes to current industrial processes.

Complete genome sequence of the dissimilatory azo reducing thermophilic bacterium Novibacillus thermophiles SG-1

With the isolation and identification of efficient azo-dye degradation bacteria, bioaugmentation with specific microbial strains has now become an effective strategy to promote the bioremediation of azo dye. However, Azo dye wastewater discharged at high temperature restricted the extensive application of the known mesophilic azoreducing microorganisms. Here we present the complete genome sequence of a bacterium capable of reducing azo dye under thermophilic condition, Novibacillus thermophiles SG-1 (=KCTC 33118^T =CGMCC 1.12363^T). The complete genome of strain SG-1 contains a circular chromosome of 3,629,225 bp with a G + C content of 50.44%. Genome analysis revealed that strain SG-1 possessed genes encoding riboflavin biosynthesis protein that would secrete riboflavin, which could act as electron shuttles to transport the electrons to extracellular azo dye in decolorization process. HPLC analysis showed that the concentration of riboflavin increased from 0.01 μM to 0.255 μM with the growth of strain SG-1 under azo dye reduction. Quantitative real-time PCR analysis further demonstrated that the gene encoding riboflavin biosynthesis protein would be involved in the azo dye decolorization. The results from this study would be beneficial to research the mechanism of anaerobic reduction of azo dye under thermophilic conditions.