Microbial and abiotic factors of flooded soil that affect redox biodegradation of lindane

Pollution induces pressure to soil microorganism; and conversely, the degradation of pollutants is reported largely regulated by the soil microbiome assembly in situ. However, the specific-dependent core taxa of degraders were barely confirmed, which is not conducive to improving the soil remediation strategy. Taking pollution of a typical organochlorine pesticide (OCP), lindane, as an example, we explored the microbial community assembly in flooded soils and simultaneously quantified the corresponding dynamics of typical soil redox processes. Contrasting initial status of microbial diversity was set up by gamma irradiation or not, with additives (acetate, NaNO_3, acetate + NaNO₃) capable of modifying microbial growth employed simultaneously. Microorganism under lindane stress was reflected by microbial adaptability within complex co-occurrence networks, wherein some environment-dependent core taxa (e.g., Clostridia, Bacteroidia, Bacilli) were highly resilient to pollution and sterilization disturbances. Lindane had higher degradation rate in irradiated soil (0.96 mg kg^-1 d^-1) than non-irradiated soil (0.83 mg kg^-1 d^-1). In non-irradiated soil, addition of acetate promoted lindane degradation and methanogenesis, whereas nitrate inhibited lindane degradation but promoted denitrification. No significant differences in lindane degradation were observed in irradiated soils, which exhibited low-diversity microbiomes in parallel to stronger Fe reduction and methanogenesis. The varied corresponding trigger effects on soil redox processes are likely due to differences of soil microbiome, specifically, deterministic or stochastic assembly, in response to pollution stress under high or low initial microbial diversity conditions. Our results improve the knowledge of the adaptability of disturbed microbiomes and their feedback on microbial functional development in OCP-polluted soils, achieving for a more reliable understanding with respect to the ecological risk of soils resided with OCPs under the fact of global microbial diversity loss.

Comprehensive analysis of the microbial communities and operational parameters of two full-scale anaerobic digestion plants treating food waste in South Korea: Seasonal variation and effect of ammonia

There are about ninety full-scale anaerobic digestion (AD) plants in South Korea that treat food waste (FW); however, the key diff ;erences in the microbial communities in different seasons and the effects of ammonia in AD remain poorly understood. In this study, the seasonal changes in microbial communities associated with operational parameters of two full-scale ADs (C and W plants) treating FW were analyzed. The organic loading rate (OLR) variability had an influence on the seasonal CH₄ yield; the W plant had a lower CH₄ yield with an unstable AD performance while the C plant had a higher CH₄ yield with a stable AD performance. It was mainly due to the substantially different NH₄⁺ concentration; the W plant had a NH₄⁺ concentration nearly 1.6 times higher compared to the C plant. The high NH₄⁺ presence in the W plant led to the dominance of class Clostridia, and methanogenesis was mostly done by hydrogenotrophs (Methanomassiliicoccus luminyensis). Additionally, the members belonging to Clostridia and Bacteroidia were found at both plants in each season (share ≥0.5%) implying their indispensable role during the anaerobic digestion of FW.

Discovered by genomics: putative reductive dehalogenases with N-terminus transmembrane helixes

Attempts for bioremediation of toxic organohalogens resulted in the identification of organohalide-respiring bacteria harbouring reductive dehalogenases (RDases) enzymes. RDases consist of the catalytic subunit (RdhA, encoded by rdhA) that does not have membrane-integral domains, and a small putative membrane anchor (RdhB, encoded by rdhB) that (presumably) locates the A subunit to the outside of the cytoplasmic membrane. Recent genomic studies identified a putative rdh gene in an uncultured deltaproteobacterial genome that was not accompanied by an rdhB gene, but contained transmembrane helixes in N-terminus. Therefore, rather than having a separate membrane anchor protein, this putative RDase is likely a hybrid of RdhA and RdhB, and directly connected to the membrane with transmembrane helixes. However, functionality of the hybrid putative RDase remains unknown. Further analysis showed that the hybrid putative rdh genes are present in the genomes of pure cultures and uncultured members of Bacteriodetes and Deltaproteobacteria, but also in the genomes of the candidate divisions. The encoded hybrid putative RDases have cytoplasmic or exoplasmic C-terminus localization, and cluster phylogenetically separately from the existing RDase groups. With increasing availability of (meta)genomes, more diverse and likely novel rdh genes are expected, but questions regarding their functionality and ecological roles remain open.

Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes

Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.

Labilibacter aurantiacus gen. nov., sp. nov., isolated from sea squirt (Styela clava) and reclassification of Saccharicrinis marinus as Labilibacter marinus comb. nov

A Gram-stain-negative, facultatively anaerobic, orange-pigmented bacterium, designated HQYD1T, was isolated from a sea squirt (Styelaclava) and characterized using a polyphasic approach. Morphologically, strain HQYD1T exhibited rods with gliding motility. This novel isolate grew optimally at 28 °C in the presence of 2-3 % (w/v) NaCl. The 16S rRNA gene sequence was most similar to [Saccharicrinis] marinus Y11T (96.3 %), followed by Saccharicinis fermentans DSM 9555T (93.8 %). The dominant fatty acids of strain HQYD1T were identified as C16 : 0, C18 : 0 and iso-C15 : 0. Major polar lipids included an unidentified lipid and a phospholipid. The major respiratory quinone was found to be MK-7, and the genomic DNA G+C content was determined to be 35.1 mol%. Based on evidence from this taxonomic study, a novel genus, Labilibacter gen. nov., is proposed in the family Marinilabiliaceae with type species Labilibacter aurantiacus sp. nov. The type strain of the type species is HQYD1T (=MCCC 1K02304T=KCTC 42583T). As [Saccharicrinis] marinus Y11T clustered phylogenetically with strain HQYD1T, we also propose [Saccharicrinis] marinus Y11T be reclassified as Labilibacter marinus comb. nov. (type strain Y11T=CICC 10837T=KCTC 42400T).

Efficient performance and the microbial community changes of submerged anaerobic membrane bioreactor in treatment of sewage containing cellulose suspended solid at 25°C

Influence of cellulose as suspended solid (SS) on the performance of submerged anaerobic membrane bioreactor (SAnMBR) was evaluated at 25°C using two types of synthetic sewage (SS contained or not). During the 110days operation, COD and BOD removal, CH4 gas recovery and cellulose accumulation were investigated in detail. The influence of cellulose as SS in sewage on the SAnMBR performance was not significant at HRT longer than12h and 65-72% of the influent COD was recovered as methane gas at HRT of 12h. At HRT of 6h, the quality of effluent got worse and the accumulation of cellulose was found in reactor. 16S rRNA analysis revealed that the microbial diversity distribution including Archaea and Bacteria changed due to the addition of SS in sewage and specific microbe for cellulose degradation such as Proteobacteria was detected. Sludge in SAnMBR could acclimate to characteristics of sewage by self-adaptation.