Arenimonas caeni sp. nov., isolated from activated sludge

Effects of Lake Erie dredged material on microbiomes in a farm soil of northwestern Ohio

Dredged materials are often considered as candidates for replenishing lost topsoils in the watersheds of rivers and lakes. This study aimed to investigate the impacts of Lake Erie dredged material on the microbial community in a farm soil of northwestern Ohio. Dredged material from the Toledo Harbor, OH was mixed with a local farm soil at ratios of 0:100, 10:90, 20:80, and 100:0 for soybean growth in a greenhouse for 123 days and was subject to 16S rRNA gene sequencing. α-Diversity analysis revealed that although the original dredged material hosted a highly diverse microbiome, soils blended with the dredged material had similar levels of bacterial diversity to 100% farm soil throughout the experiment. β-Diversity analysis demonstrated that, given the same plant status, that is, with or without soybean, blended soils had similar bacterial communities to 100% farm soil during the experiment. Furthermore, by the end of the experiment, all soils with soybeans merged into one cluster distinctive from those without the plants, indicating that the growth of plants played a dominating role in defining the structure of soil microbiomes. The majority (73.8%) of the operational taxonomy units that were unique to the original dredged material were not detected by the end of the experiment. This study demonstrates that up to 20% of the dredged material can be safely blended into the farm soil without distorting the microbial communities of the latter, implying a potential beneficial use of the dredged material for topsoil restoration.

Low C/N promotes stable partial nitrification by enhancing the cooperation of functional microorganisms in treating high-strength ammonium landfill leachate

Partial nitrification is an effective process for treating high-strength ammonium landfill leachate with low C/N ratio, for the cooperation with denitrification can save almost 40% carbon addition in biological nitrogen removal. However, high ammonia loading often causes the instability of partial nitrification process. Less carbon addition can promote the stability of partial nitrification and increase the nitrite accumulation ratio (NAR). Nevertheless, the microbial mechanisms within remain further elusive. In this study, two laboratory-scale sequencing batch reactors were constructed and operated for 125 days, which were fed with ammonia synthetic wastewater with C/N of 0.6 (CN system) and C/N of 0.0 as the control (N system). CN system performed more stably and had the highest NAR of 100%. Extracellular polymeric substances (EPS) generated from carbon source provided spatial and nutrient niches to tighten the cooperation of functional microorganisms, thus, enhanced the stability and efficiency of partial nitrification. Thauera was the dominant denitrifier in CN system. Nitrosomonas was one of the most important autotrophic ammonia oxidizing bacteria, while Paracoccus and Flavobacterium were the main heterotrophic nitrification-aerobic denitrification (HN-AD) bacteria in CN system. The enrichment of HN-AD bacteria outcompeted nitrite oxidizing bacteria (NOB), therefore leaded to higher nitrite accumulation in CN system. The findings of this study may be conducive to increasing the understanding of the microbial collaboration mechanisms of partial nitrification, thereby provides theoretical support for the improvement of biological nitrogen removal technology.

Insufficient or excessive dietary carbohydrates affect gut health through change in gut microbiota and regulation of gene expression of gut epithelial cells in grass carp (Ctenopharyngodon idella)

Dietary carbohydrate levels can affect gut health, but the roles played by gut microbiota and gut epithelial cells, and their interactions remain unclear. In this experiment, we investigated gut health, gut microbiota, and the gene expression profiles of gut epithelial cells in grass carp consuming diets with different carbohydrate levels. Compared to the moderate-carbohydrate diet, low-carbohydrate diet significantly increased the relative abundance of pathogenic bacteria (Ralstonia and Elizabethkingia) and decreased the abundance of metabolism in cofactors and vitamins, implying a dysregulated gut microbiota and compromised metabolic function. Moreover, low-carbohydrate diet inhibited the expression levels of key genes in autophagy-related pathways in gut epithelial cells, which might directly lead to reduced clearance of defective organelles and pathogenic microorganisms. These aforementioned factors may be responsible for the imperfect organization of the intestinal tract. High-carbohydrate diet also significantly increased the abundance of pathogenic bacteria (Flavobacterium), which directly contributed to a decrease in the abundance of immune system of the microbiota. Furthermore, the active pathways of staphylococcus aureus infection and complement and coagulation cascades, as well as the inhibition of the glutathione metabolism pathway were observed. Above results implied that high-carbohydrate diet might ultimately cause severe gut damage by affecting immune function of microbiota, mentioned immune-related pathways, and the antioxidant capacity. Finally, the correlation network diagram revealed strong correlations of the differentially immune-related gene major histocompatibility complex class I antigen (MR1) with Enhydrobacter and Ruminococcus_gnavus_group in low-carbohydrate diet group, and Arenimonas in high-carbohydrate diet group, respectively, suggesting that MR1 might be a central target for immune responses in gut epithelial cells induced by gut microbiota at different levels of dietary carbohydrate. All these results provided insight in the development of antagonistic probiotics and target genes to improve the utilization of carbohydrate.

Arenimonas fontis sp. nov., a bacterium isolated from Chukotka hot spring, Arctic region, Russia

A moderately thermophilic, neutrophilic, aerobic, Gram-negative bacterium, strain 3729k^T, was isolated from a thermal spring of the Chukotka Peninsula, Arctic region, Russia. It grew chemoorganoheterotrophically, utilizing proteinaceous substrates, including highly rigid keratins as well as various polysaccharides (glucomannan, locust bean gum, gum guar and xanthan gum). The major fatty acids of strain 3729k^T were iso-C_15 : 0 (60.9%), iso-C_17 : 0 (12.0%), C_16 : 0 (9.9%) and iso-C_16 : 0 (7.4%). Isoprenoid quinones were Q-8 (95%) and Q-9 (5%). The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine and three unidentified polar lipids. Strain 3729k^T was inhibited by chloramphenicol, neomycin, novobiocin, kanamycin, tetracycline, ampicillin and polymyxin B, but resistant to rifampicin, vancomycin and streptomycin. At the same time, strain 3729k^T inhibited growth of Micrococcus luteus and its genome possessed genes for antimicrobial activity against Gram-positive bacteria (a single putative bacteriocin and several secreted lysozymes and peptidoglycan lytic transglycosylases). The DNA G+C content was 69.8 mol%. 16S rRNA gene sequence-based phylogenetic analysis placed strain 3729k^T into a distinct species/genus-level branch within the family Xanthomonadaceae (Proteobacteria). Phylogenetic analysis of 120 conservative protein sequences of all Xanthomonadaceae with validly published names and publicly available genomic sequences supported a species-level position of strain 3729k^T within the genus Arenimonas. Pairwise ANI values between strain 3729k^T and other Arenimonas species were of 75-80 %, supporting the proposal of a novel species. Accordingly, Arenimonas fontis sp. nov., with the type strain 3729k^T (=VMK В-3232^Т=DSM 105847^T), was proposed.