Effects of the Denitrification Inhibitor "Procyanidins" on the Diversity, Interactions, and Potential Functions of Rhizosphere-Associated Microbiome

Long-term rice-crab coculturing leads to changes in soil microbial communities

Purpose

In order to investigate the effects of a rice-crab coculture mode and its duration on the richness and diversity of the soil microbial community.

Method

Soil from long-term rice-crab coculture mode (MY), newly established rice-crab coculture mode (OY) and rice monoculture mode (N) were used to measured soil physicochemical properties, enzyme activity and 16S and ITS soil microbial communities.

Results

The results revealed that in terms of mode, the MBC, MBN and CAT of OY were significantly greater than those of N by 10.75, 23.47 and 30.71% (p < 0.05), respectively. The richness and diversity of the soil microbial communities changed little, and there was no difference in the main species. In terms of duration, the OM, SC and PPO contents of MY were significantly greater than those of OY by 21.96, 41.89 and 11.52% (p < 0.05), respectively. The soil fungi changed significantly, and the main species were Mortierella and Pseudeurotium in genus level. The soil physicochemical properties and soil enzymes explained 93.38 and 93.66%, respectively, of the variation in the soil microbial community, and OM and DHA were the main factors influencing the change in soil biodiversity.

Conclusion

Our results suggested that long-term rice-crab coculture mode altered the richness and diversity of the soil microbial community and soil carbon sequestration.

Different oxygen affinities of methanotrophs and Comammox Nitrospira inform an electrically induced symbiosis for nitrogen loss

Aerobic methanotrophs establish a symbiotic association with denitrifiers to facilitate the process of aerobic methane oxidation coupled with denitrification (AME-D). However, the symbiosis has been frequently observed in hypoxic conditions continuing to pose an enigma. The present study has firstly characterized an electrically induced symbiosis primarily governed by Methylosarcina and Hyphomicrobium for the AME-D process in a hypoxic niche caused by Comammox Nitrospira. The kinetic analysis revealed that Comammox Nitrospira exhibited a higher apparent oxygen affinity compared to Methylosarcina. While the coexistence of comammox and AME-D resulted in an increase in methane oxidation and nitrogen loss rates, from 0.82 ± 0.10 to 1.72 ± 0.09 mmol CH4 d-1 and from 0.59 ± 0.04 to 1.30 ± 0.15 mmol N2 d-1, respectively. Furthermore, the constructed microbial fuel cells demonstrated a pronounced dependence of the biocurrents on AME-D due to oxygen competition, suggesting the involvement of direct interspecies electron transfer in the AME-D process under hypoxic conditions. Metagenomic and metatranscriptomic analysis revealed that Methylosarcina efficiently oxidized methane to formaldehyde, subsequently generating abundant NAD(P)H for nitrate reduction by Hyphomicrobium through the dissimilatory RuMP pathway, leading to CO2 production. This study challenges the conventional understanding of survival mechanism employed by AME-D symbionts, thereby contributing to the characterization responsible for limiting methane emissions and promoting nitrogen removal in hypoxic regions.

Comparison of Rhizospheric and Endophytic Bacterial Compositions between Netted and Oriental Melons

To elucidate the biological mechanism of formation of the netted pattern in melons, the characteristics of the soil bacterial community structure in the rhizosphere and of the endophytic bacteria in the stems of netted melons were analyzed. High-throughput sequencing technology was used for the analysis of plant stem and soil samples collected from netted melons (NM) and oriental melons (OM). At the phylum level, Acidobacteria, Dependentiae, and Chloroflexi were the dominant endophytic bacteria in the stems of NM only. In addition, at the genus level, the soil bacteria enriched in the rhizospheres of NM and OM were different. Five unique dominant bacterial genera, including Gaiella, Actinoplanes, norank_f__Gemmatimonadaceae, Devosia, and Bradyrhizobium, were the dominant soil bacteria unique to the rhizosphere of NM. In contrast, Mycobacterium and unclassified_f__Acetobacteraceae were the dominant soil bacteria in the rhizosphere of OM. Moreover, Hyphomicrobium, Nocardioides, norank_f__norank_o__Gaiellales, Bryobacter, unclassified_f__Pseudonocardiaceae, Pseudolabrys, norank_f__Micropepsaceae, Ideonella, Mizugakiibacter, norank_f__Vermiphilaceae, unclassified_f__Xanthobacteraceae, Bacillus, and Pseudaminobacter were the dominant endophytic bacteria in the stems of NM. In contrast, Flavobacterium, Stenotrophomonas, unclassified_f__Burkholderiaceae, Paenibacillus, Bordetella, Hephaestia, and Ideonella were the dominant endophytic bacteria in the stems of OM. The specific substances (enzymes, proteins, endogenous hormones, etc.) secreted by unique rhizospheric and endophytic bacteria, such as Bacillus and Bradyrhizobium, may activate the promoters of genes. Therefore, the expression of genes can be regulated by unique rhizospheric and endophytic bacteria for formation or nonformation of netting in melons. IMPORTANCE The study of the differential structures and functions of rhizospheric and endophytic bacterial communities between netted melon and oriental melon treatments is investigated. Our findings make a significant contribution to the literature because they are the first step in coupling the study of rhizospheric and endophytic microbial community structure to reticulation formation in netted melon. Further, we believe that this research appears to be meaningful because it provides new insights into the mechanisms of reticulation formation in netted melon in modern agricultural production.

Comparative analysis of the structure and function of rhizosphere microbiome of the Chinese medicinal herb Alisma in different regions

Rhizoma Alismatis, a commonly used traditional Chinese medicine, is the dried tuber of Alisma orientale and Alisma A. plantago-aquatica, mainly cultivated in Fujian and Sichuan provinces (China), respectively. Studies have shown that the rhizosphere microbiome is a key factor determining quality of Chinese medicinal plants. Here we applied metagenomics to investigate the rhizosphere microbiome of Alisma in Fujian and Sichuan, focusing on its structure and function and those genes involved in protostane triterpenes biosynthesis. The dominant phyla were Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria, and Gemmatimonadetes. Compared with Fujian, the rhizosphere of Sichuan has a greater α diversity and stronger microbial interactions but significantly lower relative abundance of archaea. Microbes with disease-suppressing functions were more abundant in Sichuan than Fujian, but vice versa for those with IAA-producing functions. Gemmatimonas, Anaeromyxobacter, and Pseudolabrys were the main contributors to the potential functional difference in two regions. Genes related to protostane triterpenes biosynthesis were enriched in Fujian. Steroidobacter, Pseudolabrys, Nevskia, and Nitrospira may contribute to the accumulation of protostane triterpenes in Alisma. This work fills a knowledge gap of Alisma's rhizosphere microbiome, providing a valuable reference for studying its beneficial microorganisms.