Linking rare and abundant phoD-harboring bacteria with ecosystem multifunctionality in subtropical forests: From community diversity to environmental adaptation

Microbial mechanisms for improved soil phosphorus mobilization in monoculture conifer plantations by mixing with broadleaved trees

Replanting broadleaved trees in monoculture conifer plantations has been shown to improve the ecological environment. However, not much is known about the distribution properties of soil phosphate-mobilizing bacteria (PMB) under different mixed plantings or how PMB affects biometabolism-driven phosphorus (P) bioavailability. The phoD and pqqC genes serve as molecular markers of PMB because they regulate the mobilization of organic (Po) and inorganic (Pi) P. Differences in soil bioavailable P concentration, phoD- and pqqC-harboring PMB communities, and their main regulators were analyzed using biologically-based P (BBP) and high-throughput sequencing approaches after combining coniferous trees (Pinus massoniana) and five individual broadleaved trees (Bretschneidera sinensis, Michelia maudiae, Cercidiphyllum japonicum, Manglietia conifera, and Camellia oleifera). The findings revealed that the contents of litter P, soil organic carbon (SOC), available Pi (CaCl2-P), and labile Po (Enzyme-P) were significantly higher in conifer-broadleaf mixed plantations than those in the monospecific Pinus massoniana plantations (PM), especially in the mixed stands with the introduction of Cercidiphyllum japonicum, Michelia maudiae, and Camellia oleifera. Conifer-broadleaf mixing had little effect on the abundance of phoD and pqqC genes but significantly altered species composition within the communities. Conifer-broadleaf mixing improved soil microbial habitat mainly by increasing the pH, increasing carbon source availability and nutrient content, decreasing exchangeable Fe3+ and Al3+ content, and decreasing the activation degrees of Fe and Al oxides in acidic soils. A small group of taxa (phoD: Bradyrhizobium, Tardiphaga, Nitratireductor, Mesorhizobium, Herbaspirillum, and Ralstonia; pqqC: Burkholderia, Variovorax, Bradyrhizobium, and Leptothrix) played a key role in the synthesis of P-related enzymes (e.g., alkaline phosphomonoesterase, ALP) and in lowering the levels of mineral-occluded (HCl-P) and chelated (Citrate-P) Pi. Overall, our findings highlight that mixing conifers and broadleaves could change the PMB communities that produce ALP and dissolve Pi to make P more bioavailable.

Core microbiota drive multi-functionality of the soil microbiome in the Cinnamomum camphora coppice planting

BACKGROUND

Cinnamomum camphora (L.) Presl (C. camphora) is an evergreen broad-leaved tree cultivated in subtropical China. The use of C. camphora as clonal cuttings for coppice management has become popular recently. However, little is known about the relationship between soil core microbiota and ecosystem multi-functionality under tree planting. Particularly, the effects of soil core microbiota on maintaining ecosystem multi-functionality under C. camphora coppice planting remained unclear.

MATERIALS AND METHODS

In this study, we collected soil samples from three points (i.e., the abandoned land, the root zone, and the transition zone) in the C. camphora coppice planting to investigate whether core microbiota influences ecosystem multi-functions.

RESULTS

The result showed a significant difference in soil core microbiota community between the abandoned land (AL), root zone (RZ), and transition zone (TZ), and soil ecosystem multi-functionality of core microbiota in RZ had increased significantly (by 230.8%) compared to the AL. Soil core microbiota played a more significant influence on ecosystem multi-functionality than the non-core microbiota. Moreover, the co-occurrence network demonstrated that the soil ecosystem network consisted of five major ecological clusters. Soil core microbiota within cluster 1 were significantly higher than in cluster 4, and there is also a higher Copiotrophs/Oligotrophs ratio in cluster 1. Our results corroborated that soil core microbiota is crucial for maintaining ecosystem multi-functionality. Especially, the core taxa within the clusters of networks under tree planting, with the same ecological preferences, had a significant contribution to ecosystem multi-functionality.

CONCLUSION

Overall, our results provide further insight into the linkage between core taxa and ecosystem multi-functionality. This enables us to predict how ecosystem functions respond to the environmental changes in areas under the C. camphora coppice planting. Thus, conserving the soil microbiota, especially the core taxa, is essential to maintaining the multiple ecosystem functions under the C. camphora coppice planting.

Vertical and seasonal dynamics of bacterial pathogenic communities at an aged organic contaminated site: Insights into microbial diversity, composition, interactions, and assembly processes

Under the background of the Coronavirus Disease 2019 (COVID-19) pandemic, research on pathogens deserves greater attention in the natural environment, especially in the widely distributed contaminated sites with complicated and severe organic pollution. In this study, the community composition and assembly of soil pathogens identified by the newly-developed 16S-based pipeline of multiple bacterial pathogen detection (MBPD) have been investigated on spatiotemporal scales in the selected organic polluted site. We demonstrated that the richness and diversity of the pathogenic communities were primarily controlled by soil depth, while the structure and composition of pathogenic communities varied pronouncedly with seasonal changes, which were driven by the alterations in both physiochemical parameters and organic contaminants over time. Network analysis revealed that the overwhelmingly positive interactions, identified multiple keystone species, and a well-organized modular structure maintained the stability and functionality of the pathogenic communities under environmental pressures. Additionally, the null-model analysis showed that deterministic processes dominated the pathogenic community assembly across soil profiles. In three seasons, stochasticity-dominated processes in spring and summer changed into determinism-dominated processes in winter. These findings extend our knowledge of the response of the bacterial pathogenic community to environmental disruptions brought on by organic contaminated sites.

Abundant bacterial subcommunity is structured by a stochastic process in an agricultural system with P fertilizer inputs

Soil microorganisms play an important role in agroecosystems and are related to ecosystem functioning. Nevertheless, little is understood about their community assembly and the major factors regulating stochastic and deterministic processes, particularly with respect to the comparison of abundant and rare bacterial subcommunities in agricultural systems. Here, we investigated the assembly of abundant and rare bacterial subcommunities in fields with different crops (maize and wheat) and phosphorus (P) fertilizer input at three different growth stages on the Loess Plateau. The high-throughput sequencing dataset was assessed using null and neutral community models. We found that abundant bacteria was governed by the stochastic process of homogenizing dispersal, but rare bacterial subcommunity was predominant by deterministic processes in maize and wheat fields due to broader niche breadths of abundant species. Soil nitrogen (N) and P also determined the assembly of abundant and rare soil subcommunities. The relative abundance and composition of the abundant and rare bacterial subcommunities were also influenced by soil nutrients (soil available P (AP) and NO₃^--N) and agricultural practices (P fertilization and crop cultivation). In addition, the abundant bacterial community was more susceptible to P fertilizer input than that of the rare bacteria, and a higher relative abundance of abundant bacteria was observed in the P70 treatment both in maize and wheat soils. The microbial co-occurrence network analysis indicated that the maize field and low nutrient treatment exhibited stronger associations and that the abundant bacteria showed fewer interconnections. This study provides new insights toward understanding the mechanisms for the assembly of abundant and rare bacterial taxa in dryland cropping systems, enhancing our understanding of ecosystem diversity theory in microbial ecology.

Strong linkage between nutrient-cycling functional gene diversity and ecosystem multifunctionality during winter composting with pig manure and fallen leaves

Microorganisms play important roles in element transformation and display distinct compositional changes during composting. However, little is known about the linkage between nutrient-cycling functional gene diversity and compost ecosystem multifunctionality (EMF). This study performed winter composting with pig manure and fallen leaves and evaluated the distribution patterns and ecological roles of multiple functional genes involved in nutrient cycles. Physicochemical properties and enzyme activities presented large fluctuations during composting. Absolute abundance, composition, and diversity of functional genes participating in carbon, nitrogen, phosphorus, and sulfur cycles presented distinct dynamic changes. Stronger linkage was found between enzyme activities and temperature than other physicochemical factors, whereas total nitrogen rather than other physicochemical factors displayed closer linkage with functional gene composition and diversity. EMF targeting key nutrient (i.e., carbon, nitrogen, phosphorus, and sulfur) cycles was significantly positively correlated with temperature and notably negatively correlated with functional gene diversity. Enzyme activities rather than functional gene diversity showed a greater potential effect on phosphorus availability. Consequently, the available phosphorus (AP) content increased from initial 0.50 g/kg to final 1.43 g/kg. To our knowledge, this is the first study that deciphered ecological roles of nutrient-cycling functional gene diversity during composting, and the final compost can serve as a potential phosphorus fertilizer.

Abundance and diversity of eukaryotic rather than bacterial community relate closely to the trophic level of urban lakes

Scientific understanding of biotic effects on the water trophic level is lacking for urban lakes during algal bloom development stage. Based on the Illumina MiSeq sequencing, quantitative polymerase chain reaction (PCR), and multiple statistical analyses, we estimated distribution patterns and ecological roles of planktonic bacteria and eukaryotes in urban lakes during algal bloom development stage (i.e., April, May, and June). Cyanobacteria and Chlorophyta mainly dominated algal blooms. Bacteria exhibited significantly higher absolute abundance and community diversity than eukaryotes, whereas abundance and diversity of eukaryotic rather than bacterial community relate closely to the water trophic level. Multinutrient cycling (MNC) index was significantly correlated with eukaryotic diversity rather than bacterial diversity. Stronger species replacement, broader environmental breadth, and stronger phylogenetic signal were found for eukaryotic community than for bacterial community. In contrast, bacterial community displayed stronger community stability and environmental constraint than eukaryotic community. Stochastic and differentiating processes contributed more to community assemblies of bacteria and eukaryotes. Our results emphasized that a strong linkage between planktonic diversity and MNC ensured a close relationship between planktonic diversity and the water trophic level of urban lakes. Our findings could be useful to guide the formulation and implementation of environmental lake protection measures.

Rare alkaline phosphatase-harboring bacteria mediate organic phosphorus mineralization during swine manure composting

Deciphering ecological functions of alkaline phosphatase (phoD)-harboring bacteria in composting systems is crucial but poorly understood. High-throughput sequencing, gene quantification, and statistical analyses were applied to investigate effects of abundance and diversity of phoD-harboring bacteria (PHB) on phosphorus availability during swine manure composting. Results showed that available phosphorus notably increased from 0.5 to 1.43 g kg^-1, and physicochemical properties and enzyme activities affected PHB community composition. Phylogenetic signals of PHB responded notably to temperature and phosphorus components, and stochasticity (94.2 %) dominated community assembly. Abundance and diversity of PHB directly and indirectly influenced phosphorus availability, and rare PHB mediated organic phosphorus mineralization. A phosphate-solubilizing bacterium (PSB) Pseudomonas sp. WWJ-22 isolated from compost displayed good efficiency in mineralizing lecithin, demonstrating the highest phosphorus-solubilizing level of 116.3 mg L^-1. This study highlights ecological roles of PHB on phosphorus availability and provides a potential PSB candidate for composting.

Stronger linkage of diversity-carbon decomposition for rare rather than abundant bacteria in woodland soils

Soil microbial diversity is important for maintaining ecosystem functions. However, the linkage between microbial diversity, especially rare and abundant bacterial diversity, and carbon decomposition remains largely unknown. In this study, we assessed the establishment and maintenance of rare and abundant bacterial α-diversities at the taxonomic and phylogenetic levels and their linkages with soil carbon decomposition separately in four Chinese woodlands. Compared to abundant bacteria, rare bacteria showed higher community diversity, tighter phylogenetic clustering, wider environmental breadth, stronger phylogenetic signals, and higher functional redundancy. The assembly of the abundant bacterial subcommunity was governed by stochastic (59.2%) and deterministic (41.8%) processes, whereas the assembly of the rare bacterial subcommunity was mainly dominated by deterministic processes (85.8%). Furthermore, total phosphorus, soil pH, and ammonium nitrogen balanced stochastic and deterministic processes in both rare and abundant bacterial subcommunities. Our results reveal that rare bacteria displayed stronger environmental adaptability and environmental constraint. Importantly, the α-diversities of rare taxa, rather than abundant taxa, were significantly related to carbon decomposition. This study provides a holistic understanding of biogeographic patterns of abundant and rare bacteria and their α-diversities in relation to carbon decomposition, thus helping us better predict and regulate carbon dynamics under the background of global climate change.

Responses of abundant and rare prokaryotic taxa in a controlled organic contaminated site subjected to vertical pollution-induced disturbances

Soil microbiota as the key role mediates the natural attenuation process of organic contaminated sites, and therefore illuminating the mechanisms underlying the responses of abundant and rare species is essential for understanding ecological processes, maintaining ecosystem stability, and regulating natural attenuation well. Here, we explored the distributional characteristics, ecological diversities, and co-occurrence patterns of abundant and rare prokaryotic subcommunities using 16S rRNA high-throughput sequencing in vertical soil profiles of a controlled organic contaminated site. Results showed that abundant prokaryotic taxa were widespread across all soil samples, whereas rare counterparts were unbalancedly distributed. Rare subcommunity had more taxonomic groups and higher α- and β-diversities than abundant subcommunity. Both of these two subcommunities surviving in the organic polluted site possessed the potential of degrading organic contaminants. Abundant subcommunity was little affected by abiotic factors and mainly shaped by soil depth, while rare one was sensitive to environmental disturbances and presented a non-depth-dependent structure. Co-occurrence analysis revealed that rare taxa were more situated at the center of the network and more inclined to cooperate with non-abundant species than abundant taxa, which might play crucial roles in enhancing the resilience and resistance of prokaryotic community and maintaining its structure and stability. Overall, our results suggest that abundant and rare prokaryotic subcommunities present different responses to physicochemical factors and pollution characteristics along vertical soil profiles of organic contaminated sites undergoing natural attenuation.

Spatial pattern of functional genes abundance reveals the importance of PhoD gene harboring bacterial community for maintaining plant growth in the tropical forest of Southwestern China

The concept of microbial functional genes has added a new dimension to microbial ecology research by improving the model of microbial community-ecosystem functions relationship. However, our knowledge vis-à-vis fine-scale spatial distribution pattern of functional genes and their probable impact on plant community in the hyper-diverse tropical forest ecosystem is very limited. Here, we investigated the spatial pattern of functional genes abundance (NirK, AOA, AOB, and PhoD), identified key influencing factors, and distinguished the key functional group supporting the plant community in a tropical rainforest located in Xishuangbanna. In total, 200 soil samples and vegetation data of ~4800 individuals of plants across a 1 ha study area were collected. Our results detected higher spatial variability with a maximum magnitude of abundance for PhoD gene (4.53 × 10⁷ copies) followed by NirK (2.71 × 10⁶ copies), AOA (1.97 × 10⁶ copies), and AOB (7.38 × 10⁴ copies). A strong spatial dependence was observed for PhoD and NirK over the distance of 17 and 18 m, respectively. Interestingly, the N:P stoichiometry played a critical role in structuring the spatial pattern of the most abundant PhoD gene. The significant positive and negative relationship of PhoD with N:P ratio and available phosphorus, respectively, indicated that the P-limiting environment was a driving factor for recruitment of PhoD gene community. The structural equation modeling ascertained the direct positive impact of PhoD on plant biomass and high demand of available P by plants suggesting that the organic phosphorus mineralization process is essential to maintain plant productivity by re-establishing the availability of the most limiting P nutrient. Our preliminary study improves our understanding of how microbial functional genes-environment associations could be used for monitoring soil health and its overall impact on ecosystem multifunctionality. Finally, we intend to conduct the study at a large spatial scale for achieving a holistic view.