Fungi and cercozoa regulate methane-associated prokaryotes in wetland methane emissions

Wetlands are natural sources of methane (CH4) emissions, providing the largest contribution to the atmospheric CH4 pool. Changes in the ecohydrological environment of coastal salt marshes, especially the surface inundation level, cause instability in the CH4 emission levels of coastal ecosystems. Although soil methane-associated microorganisms play key roles in both CH4 generation and metabolism, how other microorganisms regulate methane emission and their responses to inundation has not been investigated. Here, we studied the responses of prokaryotic, fungal and cercozoan communities following 5 years of inundation treatments in a wetland experimental site, and molecular ecological networks analysis (MENs) was constructed to characterize the interdomain relationship. The result showed that the degree of inundation significantly altered the CH4 emissions, and the abundance of the pmoA gene for methanotrophs shifted more significantly than the mcrA gene for methanogens, and they both showed significant positive correlations to methane flux. Additionally, we found inundation significantly altered the diversity of the prokaryotic and fungal communities, as well as the composition of key species in interactions within prokaryotic, fungal, and cercozoan communities. Mantel tests indicated that the structure of the three communities showed significant correlations to methane emissions (p < 0.05), suggesting that all three microbial communities directly or indirectly contributed to the methane emissions of this ecosystem. Correspondingly, the interdomain networks among microbial communities revealed that methane-associated prokaryotic and cercozoan OTUs were all keystone taxa. Methane-associated OTUs were more likely to interact in pairs and correlated negatively with the fungal and cercozoan communities. In addition, the modules significantly positively correlated with methane flux were affected by environmental stress (i.e., pH) and soil nutrients (i.e., total nitrogen, total phosphorus and organic matter), suggesting that these factors tend to positively regulate methane flux by regulating microbial relationships under inundation. Our findings demonstrated that the inundation altered microbial communities in coastal wetlands, and the fungal and cercozoan communities played vital roles in regulating methane emission through microbial interactions with the methane-associated community

Soil Microbial Communities in Desert Grassland around Rare Earth Mine: Diversity, Variation, and Response Patterns

Bayan Obo mine is so far the world’s largest rare earth mine. Critical concerns arise as (1) whether there is an accumulation of exogenous rare earth elements (REE) in the desert steppe on the periphery of the mine and (2) how the exogenous rare earth accumulation affects the soil microbial communities nearby. In this study, nine sample sites were set up according to their distance gradients from the mine. Illumina high-throughput sequencing targeting 16S rRNA genes were conducted. The results show that the accumulation of exogenous rare earth in the desert at the periphery of the Bayan Obo mine vary at distance gradients. Fortunately, no significant effects on the physicochemical properties of the soil were found. However, the composition of the soil microbial community changed significantly in response to the variation in distance gradient. Highly abundant microbial genera YC-ZSS-LKJ147, Subgroup_10, and Sphingomonas were positively correlated with REE, whereas Pseudomonas is negative correlated. Total phosphorus (TP) was attributed to 5.95% of the variation in microbial communities, followed by light rare earth elements (LREE, 5.39%). The study provides evidence for the ecological risks posed to soil ecosystems by the long-term accumulation of exogenous REE in the Bayan Obo mine

Inter-Trophic Networks Reveal the Central Role of Methanogens in Deposited Estuarine Soils

Exploring the distribution pattern and driving factors of methane-related microorganisms is of great significance for estimating the global methane budget, but our understanding of them is still very limited. In this study, we took a systematic soil and microbial survey along the coast of river channels in the Yellow River Delta, which included the most rapidly deposited sedimentation globally. The prokaryotes, fungi, and protists had more significant changes between two regions with distinct deposition ages than soil depths, while the accumulation of soil organic matter was the most important external driving force for the succession of microbial communities. The deposition ages of sedimental soils also altered the methanogenic and methanotrophic communities, but methanogens exhibited a greater response to environmental gradient changes than methanotrophs. Through our self-developed inter-domain ecological network platform, the inter-trophic relationships between methane-related microorganisms and other microbes have been further investigated. In the older sedimental soils, methanogens were mainly influenced by nutrient factors and tended to be negatively correlated with saprophytic fungi. In the newer sedimental soils, soil moisture, salinity, and pH primarily influenced methanogens, which tend to cooperate with some bacteria such as Firmicutes and Clostridia. This study enhances our understanding of the microbial hierarchical web in coastal wetland ecosystems. © 2023, The Authors. All rights reserved

Soil Microbial Communities in Desert Grassland around Rare Earth Mine: Diversity, Variation, and Response Patterns

Bayan Obo mine is so far the world’s largest rare earth mine. Critical concerns arise as (1) whether there is an accumulation of exogenous rare earth elements (REE) in the desert steppe on the periphery of the mine and (2) how the exogenous rare earth accumulation affects the soil microbial communities nearby. In this study, nine sample sites were set up according to their distance gradients from the mine. Illumina high-throughput sequencing targeting 16S rRNA genes were conducted. The results show that the accumulation of exogenous rare earth in the desert at the periphery of the Bayan Obo mine vary at distance gradients. Fortunately, no significant effects on the physicochemical properties of the soil were found. However, the composition of the soil microbial community changed significantly in response to the variation in distance gradient. Highly abundant microbial genera YC-ZSS-LKJ147, Subgroup_10, and Sphingomonas were positively correlated with REE, whereas Pseudomonas is negative correlated. Total phosphorus (TP) was attributed to 5.95% of the variation in microbial communities, followed by light rare earth elements (LREE, 5.39%). The study provides evidence for the ecological risks posed to soil ecosystems by the long-term accumulation of exogenous REE in the Bayan Obo mine

Steeper spatial scaling patterns of subsoil microbiota are shaped by deterministic assembly process

Although many studies have investigated the spatial scaling of microbial communities living in surface soils, very little is known about the patterns within deeper strata, nor is the mechanism behind them. Here, we systematically assessed spatial scaling of prokaryotic biodiversity within three different strata (Upper: 0‐20 cm, Middle: 20‐40 cm, and Substratum: 40‐100 cm) in a typical grassland by examining both distance‐decay (DDRs) and species‐area relationships (SARs), taxonomically and phylogenetically, as well as community assembly processes. Each layer exhibited significant biogeographic patterns in both DDR and SAR (P < 0.05), with taxonomic turnover rates higher than phylogenetic ones. Specifically, the spatial turnover rates, β and z values respectively, ranged from 0.016±0.005 to 0.023±0.005 and 0.065±0.002 to 0.077±0.004 across soil strata, and both increased with depth. Moreover, the prokaryotic community in grassland soils assembled mainly according to deterministic rather than stochastic mechanisms. By using normalized stochasticity ratio (NST) based on null model, the relative importance of deterministic ratios increased from 48.0 to 63.3% from Upper to Substratum, meanwhile a phylogenetic based method revealed average βNTI also increased with depth, from ‐5.29 to 19.5. Using variation partitioning and distance approaches, both geographic distance and soil properties were found to strongly affect biodiversity structure, the proportions increasing with depth, but spatial distance was always the main underlying factor. These indicated increasingly deterministic proportions in accelerating turnover rates for spatial assembly of prokaryotic biodiversity. Our study provided new insight on biogeography in different strata, revealing importance of assembly patterns and mechanisms of prokaryote communities in below‐surface soils

Unraveling Mechanisms and Impact of Microbial Recruitment on Oilseed Rape (Brassica napus L.) and the Rhizosphere Mediated by Plant Growth-Promoting Rhizobacteria

Plant growth-promoting rhizobacteria (PGPR) are noticeably applied to enhance plant nutrient acquisition and improve plant growth and health. However, limited information is available on the compositional dynamics of rhizobacteria communities with PGPR inoculation. In this study, we investigated the effects of three PGPR strains, Stenotrophomonas rhizophila, Rhodobacter sphaeroides, and Bacillus amyloliquefaciens on the ecophysiological properties of Oilseed rape (Brassica napus L.), rhizosphere, and bulk soil; moreover, we assessed rhizobacterial community composition using high-throughput Illumina sequencing of 16S rRNA genes. Inoculation with S. rhizophila, R. sphaeroides, and B. amyloliquefaciens, significantly increased the plant total N (TN) (p &lt; 0.01) content. R. sphaeroides and B. amyloliquefaciens selectively enhanced the growth of Pseudomonadacea and Flavobacteriaceae, whereas S. rhizophila could recruit diazotrophic rhizobacteria, members of Cyanobacteria and Actinobacteria, whose abundance was positively correlated with inoculation, and improved the transformation of organic nitrogen into inorganic nitrogen through the promotion of ammonification. Initial colonization by PGPR in the rhizosphere affected the rhizobacterial community composition throughout the plant life cycle. Network analysis indicated that PGPR had species-dependent effects on niche competition in the rhizosphere. These results provide a better understanding of PGPR-plant-rhizobacteria interactions, which is necessary to develop the application of PGPR

Unraveling Mechanisms and Impact of Microbial Recruitment on Oilseed Rape (<i>Brassica napus</i> L.) and the Rhizosphere Mediated by Plant Growth-Promoting Rhizobacteria

Plant growth-promoting rhizobacteria (PGPR) are noticeably applied to enhance plant nutrient acquisition and improve plant growth and health. However, limited information is available on the compositional dynamics of rhizobacteria communities with PGPR inoculation. In this study, we investigated the effects of three PGPR strains, Stenotrophomonas rhizophila, Rhodobacter sphaeroides, and Bacillus amyloliquefaciens on the ecophysiological properties of Oilseed rape (Brassica napus L.), rhizosphere, and bulk soil; moreover, we assessed rhizobacterial community composition using high-throughput Illumina sequencing of 16S rRNA genes. Inoculation with S. rhizophila, R. sphaeroides, and B. amyloliquefaciens, significantly increased the plant total N (TN) (p R. sphaeroides and B. amyloliquefaciens selectively enhanced the growth of Pseudomonadacea and Flavobacteriaceae, whereas S. rhizophila could recruit diazotrophic rhizobacteria, members of Cyanobacteria and Actinobacteria, whose abundance was positively correlated with inoculation, and improved the transformation of organic nitrogen into inorganic nitrogen through the promotion of ammonification. Initial colonization by PGPR in the rhizosphere affected the rhizobacterial community composition throughout the plant life cycle. Network analysis indicated that PGPR had species-dependent effects on niche competition in the rhizosphere. These results provide a better understanding of PGPR-plant-rhizobacteria interactions, which is necessary to develop the application of PGPR

Evolutionary History and Functional Diversification of the <i>JmjC</i> Domain-Containing Histone Demethylase Gene Family in Plants

Histone demethylases containing JumonjiC (JmjC) domains regulate gene transcription and chromatin structure by changing the methylation status of lysine residues and play an important role in plant growth and development. In this study, a total of 332 JmjC family genes were identified from 21 different plant species. The evolutionary analysis results showed that the JmjC gene was detected in each species, that is, the gene has already appeared in algae. The phylogenetic analysis showed that the KDM3/JHDM2 subfamily genes may have appeared when plants transitioned from water to land, but were lost in lycophytes (Selaginella moellendorffii). During the evolutionary process, some subfamily genes may have been lost in individual species. According to the analysis of the conserved domains, all of the plant JmjC genes contained a typical JmjC domain, which was highly conserved during plant evolution. The analysis of cis-acting elements showed that the promoter region of the JmjC gene was rich in phytohormones and biotic and abiotic stress-related elements. The transcriptome data analysis and protein interaction analyses showed that JmjC genes play an important role in plant growth and development. The results clarified the evolutionary history of JmjC family genes in plants and lay the foundation for the analysis of the biological functions of JmjC family genes