Increasing Inundation Frequencies Enhance the Stochastic Process and Network Complexity of the Soil Archaeal Community in Coastal Wetlands

Enhancement of nitrogen on core taxa recruitment by Penicillium oxalicum stimulated microbially-driven soil formation in bauxite residue

Microbially-driven soil formation process is an emerging technology for the ecological rehabilitation of alkaline tailings. However, the dominant microorganisms and their specific roles in soil formation processes remain unknown. Herein, a 1-year field-scale experiment was applied to demonstrate the effect of nitrogen input on the structure and function of the microbiome in alkaline bauxite residue. Results showed that the contents of nutrient components were increased with Penicillium oxalicum (P. oxalicum) incorporation, as indicated by the increasing of carbon and nitrogen mineralization and enzyme metabolic efficiency. Specifically, the increasing enzyme metabolic efficiency was associated with nitrogen input, which shaped the microbial nutrient acquisition strategy. Subsequently, we evidenced that P. oxalicum played a significant role in shaping the assemblages of core bacterial taxa and influencing ecological functioning through intra- and cross-kingdom network analysis. Furthermore, a recruitment experiment indicated that nitrogen enhanced the enrichment of core microbiota (Nitrosomonas, Bacillus, Pseudomonas, and Saccharomyces) and may provide benefits to fungal community bio-diversity and microbial network stability. Collectively, these results demonstrated nitrogen-based coexistence patterns among P. oxalicum and microbiome and revealed P. oxalicum-mediated nutrient dynamics and ecophysiological adaptations in alkaline microhabitats. It will aid in promoting soil formation and ecological rehabilitation of bauxite residue. ENVIRONMENT IMPLICATION: Bauxite residue is a highly alkaline solid waste generated during the Bayer process for producing alumina. Attempting to transform bauxite residue into a stable soil-like substrate using low-cost microbial resources is a highly promising engineering. However, the dominant microorganisms and their specific roles in soil formation processes remain unknown. In this study, we evidenced the nitrogen-based coexistence patterns among Penicillium oxalicum and microbiome and revealed Penicillium oxalicum-mediated nutrient dynamics and ecophysiological adaptations in alkaline microhabitats. This study can improve the understanding of core microbes' assemblies that affect the microbiome physiological traits in soil formation processes.

An Assessment of Human Opportunistic Pathogenic Bacteria on Daily Necessities in Nanjing City during Plum Rain Season

The plum rain season is a special climatic phenomenon in east Asia, which is characterized by persistent rainfall, a high temperature, and humidity, providing suitable environmental conditions for certain pathogenic bacteria, thus increasing the incidence of respiratory, gastrointestinal, and urinary diseases. However, studies on human opportunistic pathogenic bacteria communities during the plum rain season are still limited. In this study, the characteristics of human opportunistic pathogenic bacterial communities on daily necessities during the non-plum and plum rain seasons were investigated using high-throughput sequencing technology. The results revealed that the relative abundance of human opportunistic pathogenic bacteria was higher in the plum rain season (cotton cloth: 2.469%, electric bicycles: 0.724%, rice: 3.737%, and washbasins: 5.005%) than in the non-plum rain season (cotton cloth: 1.425%, electric bicycles: 0.601%, rice: 2.426%, and washbasins: 4.801%). Both temperature and relative humidity affected human opportunistic pathogenic bacterial communities. Stochastic processes dominated the assembly process of human opportunistic pathogenic bacterial communities, and undominated processes prevailed. The stability of the co-occurrence network was higher in the non-plum rain season than that in the plum rain season. In addition, the proportion of deterministic processes showed the same trend as the complexity of the co-occurrence network.

The influence of tide-brought nutrients on microbial carbon metabolic profiles of mangrove sediments

Mangrove ecosystems in the intertidal zone are continually affected by tidal inundation, but the impact of tidal-driven nutrient inputs upon bacterial communities and carbon metabolic features in mangrove surface sediments remains underexplored, and the differences in such impacts across backgrounds are not known. Here, two mangrove habitats with contrasting nutrient backgrounds in Shenzhen Bay and Daya Bay in Shenzhen City, China, respectively, were studied to investigate the effects of varying tidal nutrient inputs (especially dissolved inorganic nitrogen and PO43--P) on bacterial community composition and functioning in sediment via field sampling, 16S rDNA amplicon sequencing, and the quantitative potential of microbial element cycling. Results showed that tidal input increased Shenzhen Bay mangrove's eutrophication level whereas it maintained the Daya Bay mangrove's relatively oligotrophic status. Dissolved inorganic nitrogen and PO43--P levels in Shenzhen Bay were respectively 12.6-39.6 and 7.3-29.1 times higher than those in Daya Bay (p < 0.05). In terms of microbial features, Desulfobacteraceae was the dominant family in Shenzhen Bay, while the Anaerolineaceae family dominated in Daya Bay. Co-occurrence network analysis revealed more interconnected and complex microbial networks in Shenzhen Bay. The quantitative gene-chip analysis uncovered more carbon-related functional genes (including carbon degradation and fixation) enriched in Shenzhen Bay's sediment microbial communities than Daya Bay's. Partial least squares path modeling indicated that tidal behavior directly affected mangrove sediments' physicochemical characteristics, with cascading effects shaping microbial diversity and C-cycling function. Altogether, these findings demonstrate that how tides influence the microbial carbon cycle in mangrove sediments is co-correlated with the concentration of nutrient inputs and background status of sediment. This work offers an insightful lens for better understanding bacterial community structure and carbon metabolic features in mangrove sediments under their tidal influences. It provides a theoretical basis to better evaluate and protect mangroves in the context of global change.

Depth-Dependent Distribution of Prokaryotes in Sediments of the Manganese Crust on Nazimov Guyots of the Magellan Seamounts

Deep ocean polymetallic nodules, rich in cobalt, nickel, and titanium which are commonly used in high-technology and biotechnology applications, are being eyed for green energy transition through deep-sea mining operations. Prokaryotic communities underneath polymetallic nodules could participate in deep-sea biogeochemical cycling, however, are not fully described. To address this gap, we collected sediment cores from Nazimov guyots, where polymetallic nodules exist, to explore the diversity and vertical distribution of prokaryotic communities. Our 16S rRNA amplicon sequencing data, quantitative PCR results, and phylogenetic beta diversity indices showed that prokaryotic diversity in the surficial layers (0-8 cm) was > 4-fold higher compared to deeper horizons (8-26 cm), while heterotrophs dominated in all sediment horizons. Proteobacteria was the most abundant taxon (32-82%) across all sediment depths, followed by Thaumarchaeota (4-37%), Firmicutes (2-18%), and Planctomycetes (1-6%). Depth was the key factor controlling prokaryotic distribution, while heavy metals (e.g., iron, copper, nickel, cobalt, zinc) can also influence significantly the downcore distribution of prokaryotic communities. Analyses of phylogenetic diversity showed that deterministic processes governing prokaryotic assembly in surficial layers, contrasting with stochastic influences in deep layers. This was further supported from the detection of a more complex prokaryotic co-occurrence network in the surficial layer which suggested more diverse prokaryotic communities existed in the surface vs. deeper sediments. This study expands current knowledge on the vertical distribution of benthic prokaryotic diversity in deep sea settings underneath polymetallic nodules, and the results reported might set a baseline for future mining decisions.

Community assembly of comammox Nitrospira in coastal wetlands across southeastern China

Complete ammonia oxidizers (comammox Nitrospira) are ubiquitous in coastal wetland sediments and play an important role in nitrification. Our study examined the impact of habitat modifications on comammox Nitrospira communities in coastal wetland sediments across tropical and subtropical regions of southeastern China. Samples were collected from 21 coastal wetlands in five provinces where native mudflats were invaded by Spartina alterniflora and subsequently converted to aquaculture ponds. The results showed that comammox Nitrospira abundances were mainly influenced by sediment grain size rather than by habitat modifications. Compared to S. alterniflora marshes and native mudflats, aquaculture pond sediments had lower comammox Nitrospira diversity, lower clade A.1 abundance, and higher clade A.2 abundance. Sulfate concentration was the most important factor controlling the diversity of comammox Nitrospira. The response of comammox Nitrospira community to habitat change varied significantly by location, and environmental variables accounted for only 11.2% of the variations in community structure across all sites. In all three habitat types, dispersal limitation largely controlled the comammox Nitrospira community assembly process, indicating the stochastic nature of these sediment communities in coastal wetlands. IMPORTANCE Comammox Nitrospira have recently gained attention for their potential role in nitrification and nitrous oxide (N2O) emissions in soil and sediment. However, their distribution and assembly in impacted coastal wetland are poorly understood, particularly on a large spatial scale. Our study provides novel evidence that the effects of habitat modification on comammox Nitrospira communities are dependent on the location of the wetland. We also found that the assembly of comammox Nitrospira communities in coastal wetlands was mainly governed by stochastic processes. Nevertheless, sediment grain size and sulfate concentration were identified as key variables affecting comammox Nitrospira abundance and diversity in coastal sediments. These findings are significant as they advance our understanding of the environmental adaptation of comammox Nitrospira and how future landscape modifications may impact their abundance and diversity in coastal wetlands.

Roles of sulfate-reducing bacteria in sustaining the diversity and stability of marine bacterial community

Microbes play central roles in ocean food webs and global biogeochemical processes. Yet, the information available regarding the highly diverse bacterial communities in these systems is not comprehensive. Here we investigated the diversity, assembly process, and species coexistence frequency of bacterial communities in seawater and sediment across ∼600 km of the eastern Chinese marginal seas using 16S rRNA gene amplicon sequencing. Our analyses showed that compared with seawater, bacterial communities in sediment possessed higher diversity and experienced tight phylogenetic distribution. Neutral model analysis showed that the relative contribution of stochastic processes to the assembly process of bacterial communities in sediment was lower than that in seawater. Functional prediction results showed that sulfate-reducing bacteria (SRB) were enriched in the core bacterial sub-communities. The bacterial diversities of both sediment and seawater were positively associated with the relative abundance of SRB. Co-occurrence analysis showed that bacteria in seawater exhibited a more complex interaction network and closer co-occurrence relationships than those in sediment. The SRB of seawater were centrally located in the network and played an essential role in sustaining the complex network. In addition, further analysis indicated that the SRB of seawater helped maintain the high stability of the bacterial network. Overall, this study provided further comprehensive information regarding the characteristics of bacterial communities in the ocean, and provides new insights into keystone taxa and their roles in sustaining microbial diversity and stability in ocean.

Deterministic processes dominate archaeal community assembly from the Pearl River to the northern South China Sea

Archaea play a significant role in the biogeochemical cycling of nutrients in estuaries. However, comprehensive researches about their assembly processes remain notably insufficient. In this study, we systematically examined archaeal community dynamics distinguished between low-salinity and high-salinity groups in water and surface sediments over a 600-kilometer range from the upper Pearl River (PR) to the northern South China Sea (NSCS). Neutral community model analysis together with null model analysis showed that their C-score values were greater than 2, suggesting that deterministic processes could dominate the assembly of those planktonic or benthic archaeal communities at both the low-salinity and high-salinity sites. And deterministic processes contributed more in the low-salinity than high-salinity environments from the PR to the NSCS. Furthermore, through the co-occurrence network analysis, we found that the archaeal communities in the low-salinity groups possessed closer interactions and higher proportions of negative interactions than those in the high-salinity groups, which might be due to the larger environmental heterogeneities reflected by the nutrient concentrations of those low-salinity samples. Collectively, our work systematically investigated the composition and co-occurrence networks of archaeal communities in water as well as sediments from the PR to the NSCS, yielding new insights into the estuary's archaeal community assembly mechanisms.

Plant Species-Driven Distribution of Individual Clades of Comammox Nitrospira in a Subtropical Estuarine Wetland

Plant species play a crucial role in mediating the activity and community structure of soil microbiomes through differential inputs of litter and rhizosphere exudates, but we have a poor understanding of how plant species influence comammox Nitrospira, a newly discovered ammonia oxidizer with pivotal functionality. Here, we investigate the abundance, diversity, and community structure of comammox Nitrospira underneath five plant species and a bare tidal flat at three soil depths in a subtropical estuarine wetland. Plant species played a critical role in driving the distribution of individual clades of comammox Nitrospira, explaining 59.3% of the variation of community structure. Clade A.1 was widely detected in all samples, while clades A.2.1, A.2.2, A.3 and B showed plant species-dependent distribution patterns. Compared with the native species Cyperus malaccensis, the invasion of Spartina alterniflora increased the network complexity and changed the community structure of comammox Nitrospira, while the invasive effects from Kandelia obovata and Phragmites australis were relatively weak. Soil depths significantly influenced the community structure of comammox Nitrospira, but the effect was much weaker than that from plant species. Altogether, our results highlight the previously unrecognized critical role of plant species in driving the distribution of comammox Nitrospira in a subtropical estuarine wetland.

Spartina alterniflora invasion has a greater impact than non-native species, Phragmites australis and Kandelia obovata, on the bacterial community assemblages in an estuarine wetland

The invasion of Spartina alterniflora poses a serious threat to the sustainability of native ecosystems worldwide. However, compared with other non-native plants (e.g., Phragmites australis and Kandelia obovata), how Spartina alterniflora invasion influences the community structure of bacteria and their assembly processes and functionality remains elusive. Here, we characterized the diversity, community structure, assembly processes and functional guilds of bacteria underneath five plant species and a bare tidal flat at three soil depths in an estuarine wetland. We found that plant species played a more important role than soil depth in mediating the bacterial community structure. Compared with bare tidal flats, the native species Cyperus malaccensis, rather than Scirpus triqueter, significantly changed the bacterial community structure. However, S. alterniflora invasion increased bacterial alpha diversity and significantly altered the bacterial community structure by enriching Chloroflexi, Bacteroidetes and Firmicutes while reducing Acidobacteria, Nitrospirae and Gemmatimonadetes. The invasion of P. australis and translocation of K. obovata had less pronounced effects on the bacterial community structure. Total carbon, total nitrogen and salinity were the key environmental factors mediating the bacterial community structure. Overall of all the non-native plant species, the invasion of S. alterniflora increased the relative importance of stochastic processes in the assembly of bacterial communities, and shifted the bacterial functional profiles by stimulating sulfur cycling groups and suppressing nitrogen cycling groups. Altogether, our results suggest that S. alterniflora invasion has a greater effect than P. australis invasion or K. obovata translocation on the profiles and assembly processes of the bacterial communities, with important implications for soil biogeochemical processes in coastal wetlands.