Antimony precipitation and removal by antimony hyper resistant strain Achromobacter sp. 25-M.

Microbes have been confirmed to play key role in biogeochemistry of antimony. However, the impact of indigenous bacteria (from active mines) on the behavior of dissolved antimony remained poorly understood. In current study, the hyper antimony-resistant strain, Achromobacter sp. 25-M, isolated from the world largest antimony deposit, Xikuangshan antimony deposit, was evaluated for its role in dissolved Sb(V) and Sb(III) precipitation and removal. Despite of the high resistance to Sb(III) (up to 50 mM), the facultative alkaliphile, 25-M was not capable of Sb(III) oxidation. Meanwhile 25-M can produce high amount of exopolymeric substance (EPS) with the presence of Sb, which prompted us to investigate the potential role of EPS in the precipitation and removal of Sb. To this end, 2 mM of Sb(III) and Sb(V) were added into the experimental systems with and without 25-M to discern the interaction mechanism between microbe and antimony. After 96 hrs' incubation, 88% [1.73 mM (210 mg/L)] of dissolved Sb(V) and 80% [1.57 mM (190 mg/L)] of dissolved Sb(III) were removed. X-ray diffraction and energy dispersive spectroscopy analysis confirmed the formation of valentinite (Sb2O3) in Sb(III) amended system and a solitary Sb(V) mineral mopungite [NaSb(OH)6] in Sb(V) amended group with microbes. Conversely, no precipitate was detected in abiotic systems. Morphologically valentinite was bowtie and mopungite was pseudo-cubic as indicated by scanning electronic microscopy. EPS was subjected to fourier transform infrared (FT-IR) analysis. FT-IR analysis suggested that -OH and -COO groups were responsible for the complexation and ligand exchange with Sb(III) and Sb(V), respectively. Additionally, the C-H group and N-H group could be involved in π-π interaction and chelation with Sb species. All these interactions between Sb and functional groups in EPS may subsequently favore the formation of valentinite and mopungite. Collectively, current results suggested that EPS play fundamental role in bioprecipitation of Sb, which offered a new strategy in Sb bioremediation.

Diverse Bathyarchaeotal Lineages Dominate Archaeal Communities in the Acidic Dajiuhu Peatland, Central China.

Bathyarchaeota are believed to have roles in the carbon cycle in marine systems. However, the ecological knowledge of Bathyarchaeota is limited in peatland ecosystems. Here, we investigated the vertical distribution of Bathyarchaeota community structure using quantitative PCR and high-throughput sequencing technology of ribosomal 16S rRNA gene integrated with detailed chemical profiling in the Dajiuhu Peatland, central China. Eight archaeal phyla were observed in peat samples, which mainly composed of Bathyarchaeota with a mean relative abundance about 88%, followed by Thaumarchaeota (9%). Bathyarchaeota were further split into 17 subgroups, and some subgroups showed habitat specificity to peat horizons with distinct lithological and physicochemical properties, for example, Bathy-6 and Bathy-15 had preference for the acrotelm, Bathy-5b, Bathy-16, and Bathy-19 were enriched in the catotelm, Bathy-5a, Bathy-8, and Bathy-11 were specific for the clay horizon. This spatial distribution pattern of archaeal communities along peat profile was mainly influenced by water content as indicated by RDA ordination and permutational MANOVA, whereas organic matter content exclusively affected Bathyarchaeota distribution along the peat profile significantly. The abundance of archaeal 16S rRNA genes ranged from 105 to 107 copies per gram dry sediment, and the highest archaeal biomass was observed in the periodically oxic mesotelm horizon with more dynamic archaeal interaction relationship as indicated by the network analysis. Bathyarchaeota dominated the archaeal interaction network with 82% nodes, 96% edges, and 71% keystone species. Our results provide an overview of the archaeal population, community structure, and relationship with environmental factors that affect the vertical distribution of archaeal communities and emphasize the ecology of bathyarchaeotal lineages in terrestrial peatland ecosystems.

Nebela jiuhuensis nov. sp. (Amoebozoa; Arcellinida; Hyalospheniidae): A New Member of the Nebela saccifera - equicalceus - ansata Group Described from Sphagnum Peatlands in South-Central China.

Hyalospheniids are among the most common and conspicuous testate amoebae in high-latitude peatlands and forest humus. These testate amoebae were widely studied as bioindicators and are increasingly used as models in microbial biogeography. However, data on their diversity and ecology are still very unevenly distributed geographically: notably, data are lacking for low-latitude peatlands. We describe here a new species, Nebela jiuhuensis, from peatlands near the Middle Yangtze River reach of south-central China with characteristic morphology. The test (shell) has hollow horn-like lateral extensions also found in N. saccifera, N. equicalceus (=N. hippocrepis), and N. ansata, three large species restricted mostly to Sphagnum peatlands of Eastern North America. Mitochondrial cytochrome oxidase (COI) data confirm that N. jiuhuensis is closely related to the morphologically very similar North American species N. saccifera and more distantly to N. ansata within the N. penardiana group. These species are all found in wet mosses growing in poor fens. Earlier reports of morphologically similar specimens found in South Korea peatlands suggest that N. jiuhuensis may be distributed in comparable peatlands in Eastern Asia (China and Korea). The discovery of such a conspicuous new species in Chinese peatlands suggests that many new testate amoebae species are yet to be discovered, including potential regional endemics. Furthermore, human activities (e.g., drainage, agriculture, and pollution) have reduced the known habitat of N. jiuhuensis, which can thus be considered as locally endangered. We, therefore, suggest that this very conspicuous micro-organism with a probably limited geographical distribution and specific habitat requirement should be considered as a flagship species for microbial biogeography as well as local environmental conservation and management.

Global hotspots and trends in microbial-mediated grassland carbon cycling: a bibliometric analysis.

Grasslands are among the most widespread environments on Earth, yet we still have poor knowledge of their microbial-mediated carbon cycling in the context of human activity and climate change. We conducted a systematic bibliometric analysis of 1,660 literature focusing on microbial-mediated grassland carbon cycling in the Scopus database from 1990 to 2022. We observed a steep increase in the number of multidisciplinary and interdisciplinary studies since the 2000s, with focus areas on the top 10 subject categories, especially in Agricultural and Biological Sciences. Additionally, the USA, Australia, Germany, the United Kingdom, China, and Austria exhibited high levels of productivity. We revealed that the eight papers have been pivotal in shaping future research in this field, and the main research topics concentrate on microbial respiration, interaction relationships, microbial biomass carbon, methane oxidation, and high-throughput sequencing. We further highlight that the new research hotspots in microbial-mediated grassland carbon cycling are mainly focused on the keywords "carbon use efficiency," "enzyme activity," "microbial community," and "high throughput sequencing." Our bibliometric analysis in the past three decades has provided insights into a multidisciplinary and evolving field of microbial-mediated grassland carbon cycling, not merely summarizing the literature but also critically identifying research hotspots and trends, the intellectual base, and interconnections within the existing body of collective knowledge and signposting the path for future research directions.

Testate amoebae (Protozoa) in lakes of the Qinghai-Tibet Plateau: Biodiversity, community structures, and protozoic biosilicification in relation to environmental properties and climate warming.

The Qinghai-Tibet Plateau (QTP) is characterized by a vast number of frozen and unfrozen freshwater reservoirs, which is why it is also called "the third pole" of the Earth or "Asian Water Tower". We analyzed testate amoeba (TA) biodiversity and corresponding protozoic biosilicification in lake sediments of the QTP in relation to environmental properties (freshwater conditions, elevation, and climate). As TA are known as excellent bio-indicators, our results allowed us to derive conclusions about the influence of climate warming on TA communities and microbial biogeochemical silicon (Si) cycling. We found a total of 113 TA taxa including some rare and one unknown species in the analyzed lake sediments of the QTP highlighting the potential of this remote region for TA biodiversity. >1/3 of the identified TA taxa were relatively small (<30 µm) reflecting the relatively harsh environmental conditions in the examined lakes. TA communities were strongly affected by physico-chemical properties of the lakes, especially water temperature and pH, but also elevation and climate conditions (temperature, precipitation). Our study reveals climate-related changes in TA biodiversity with consequences for protozoic biosilicification. As the warming trend in the QTP is two to three times faster compared to the global average, our results provide not only deeper insights into the relations between TA biodiversity and environmental properties, but also predictions of future developments in other regions of the world. Moreover, our results provide fundamental data for paleolimnological reconstructions. Thus, examining the QTP is helpful to understand microbial biogeochemical Si cycling in the past, present, and future.

Deconstructing the Dimensions of Mycobiome Fingerprints in Luohandu Cave, Guilin, Southern China.

Subterranean karst caves are windows into the terrestrial subsurface to deconstruct the dimensions of mycobiome fingerprints. However, impeded by the constraints of remote locations, the inaccessibility of specimens and technical limitations, the mycobiome of subterranean karst caves has remained largely unknown. Weathered rock and sediment samples were collected from Luohandu cave (Guilin, Southern China) and subjected to Illumina Hiseq sequencing of ITS1 genes. A total of 267 known genera and 90 known orders in 15 phyla were revealed in the mycobiomes. Ascomycota dominated all samples, followed by Basidiomycota and Mortierellomycota. The sediments possessed the relatively highest alpha diversity and were significantly different from weathered rocks according to the diversity indices and richness metrics. Fifteen families and eight genera with significant differences were detected in the sediment samples. The Ca/Mg ratio appeared to significantly affect the structure of the mycobiome communities. Ascomycota appeared to exert a controlling influence on the mycobiome co-occurrence network of the sediments, while Ascomycota and Basidiomycota were found to be the main phyla in the mycobiome co-occurrence network of weathered rocks. Our results provide a more comprehensive dimension to the mycobiome fingerprints of Luohandu cave and a new window into the mycobiome communities and the ecology of subterranean karst cave ecosystems.

Keystone Taxa and Predictive Functional Analysis of Sphagnum palustre Tank Microbiomes in Erxianyan Peatland, Central China.

Sphagnum is a fundamental ecosystem of engineers, including more than 300 species around the world. These species host diverse microbes, either endosymbiotic or ectosymbiotic, and are key to carbon sequestration in peatland ecosystems. However, the linkages between different types of Sphagnum and the diversity and ecological functions of Sphagnum-associated microbiomes are poorly known, and so are their joint responses to ecological functions. Here, we systematically investigated endophytes in Sphagnum palustre via next-generation sequencing (NGS) techniques in the Erxianyan peatland, central China. The total bacterial microbiome was classified into 38 phyla and 55 classes, 122 orders and 490 genera. The top 8 phyla of Proteobacteria (33.69%), Firmicutes (11.94%), Bacteroidetes (9.42%), Actinobacteria (6.53%), Planctomycetes (6.37%), Gemmatimonadetes (3.05%), Acidobacteria (5.59%) and Cyanobacteria (1.71%) occupied 78.31% of total OTUs. The core microbiome of S. palustre was mainly distributed mainly in 7 phyla, 9 classes, 15 orders, 22 families and 43 known genera. There were many differences in core microbiomes compared to those in the common higher plants. We further demonstrate that the abundant functional groups have a substantial potential for nitrogen fixation, carbon cycle, nitrate metabolism, sulfate respiration and chitinolysis. These results indicate that potential ecological function of Sphagnum palustre in peatlands is partially rooted in its microbiomes, and that incorporating into functional groups of Sphagnum-associated microbiomes can promote mechanistic understanding of Sphagnum ecology in subalpine peatlands.

Contrasting bacterial communities and their assembly processes in karst soils under different land use.

Structure and assembly processes of soil bacterial communities under different land use at karst areas remained poorly understood to date. To address this issue, soil samples from arable land and pristine forest over a karst cave, located in the acid rain impacted area, Hubei province, were collected and subjected to high-throughput sequencing and multivariate statistical analysis. Bacterial communities and functions remarkably distinguished between soils under different land use. Both edaphic properties (the content of SO42-, C/N, pH, TN) and weathering processes, such as Si concentration, Mg/Al and Ca/Al, significantly impacted on soil bacterial community structures. Variable selections were predominant ecological processes, and pH and SO42- concentration were of significance in community assembly. Random molecular ecological network analysis revealed a more stable and complex microbial network in the forest ecosystem, which can quickly response to environmental change. Forest soil bacteria were mainly phototrophs, involving in C and N cycles, whereas those in arable soils were mainly chemoheterotrophs, capable of degrading organic fertilizers due to anthropogenic activities as confirmed by the analysis of keystone taxa, indicators and functional prediction. These results reveal that land use constructed soil bacterial communities in different aspects such as the structure, potential functions, microbial interactions and correlations with environmental variables. To our knowledge, this is the first report on bacterial community assembly in karst soils under different land use which enhances our understanding about how land use impact on microbial interaction and community assembly processes.

Diversity of Fungal Communities in Heshang Cave of Central China Revealed by Mycobiome-Sequencing.

Deciphering of the mycobiome in pristine karst caves has been impeded by constraints of remote locations, inaccessibility to specimens and technical limitations, which greatly restricted in-depth understanding of mycobiomes in subterranean ecosystem. Here, mycobiomes of Heshang Cave in south-western karst region of China were investigated by Illumina HiSeq sequencing of fungal rRNA-ITS1 gene across different habitats. In total 793,502 ITS1 reads and 2,179 OTUs from 778 Mb reads after stringent quality control (Q30) and 453 genera, 72 orders and 19 classes within 6 phyla were detected. Ascomycota (42% OTUs) dominated across the five habitats. Shannon-Wiener index varied from 1.25 to 7.62 and community richness was highest in drip waters, followed by weathered rocks, bat guanos, sediments, and air samples. Mycobiomes displayed specificity to five habitats and more distinct OTUs were found in weathered rocks (12%) and drip waters (9%). In contrast, only 6.60% core OTUs were shared by five habitats. Notably, weathered rocks possessed more indicator groups and were revealed for the first time to be dominated by Sordariomycetes (43%). The community richness of air mycobiomes increased from cave entrance to the innermost part and dominated by the indicator groups of Penicillium mallochii (>30%) and P. herquei (>9%). Our work represents the largest attempt to date to a systematical investigation of oligotrophic solution-cave-associated mycobiomes in China. Our discovery of high diversity of mycobiomes in Heshang Cave also suggests that eukaryotic microorganisms may play a crucial role in subsurface environments.

Distribution of Bathyarchaeota Communities Across Different Terrestrial Settings and Their Potential Ecological Functions.

High abundance and widespread distribution of the archaeal phylum Bathyarchaeota in marine environment have been recognized recently, but knowledge about Bathyarchaeota in terrestrial settings and their correlation with environmental parameters is fairly limited. Here we reported the abundance of Bathyarchaeota members across different ecosystems and their correlation with environmental factors by constructing 16S rRNA clone libraries of peat from the Dajiuhu Peatland, coupling with bioinformatics analysis of 16S rRNA data available to date in NCBI database. In total, 1456 Bathyarchaeota sequences from 28 sites were subjected to UniFrac analysis based on phylogenetic distance and multivariate regression tree analysis of taxonomy. Both phylogenetic and taxon-based approaches showed that salinity, total organic carbon and temperature significantly influenced the distribution of Bathyarchaeota across different terrestrial habitats. By applying the ecological concept of 'indicator species', we identify 9 indicator groups among the 6 habitats with the most in the estuary sediments. Network analysis showed that members of Bathyarchaeota formed the "backbone" of archaeal community and often co-occurred with Methanomicrobia. These results suggest that Bathyarchaeota may play an important ecological role within archaeal communities via a potential symbiotic association with Methanomicrobia. Our results shed light on understanding of the biogeography, potential functions of Bathyarchaeota and environment conditions that influence Bathyarchaea distribution in terrestrial settings.

The Relationship between pH and Bacterial Communities in a Single Karst Ecosystem and Its Implication for Soil Acidification.

Enhanced monsoon duration and soil acidification from acid rain are expected to impact the distribution of microbial communities in surface and subsurface environments, although these impacts are poorly understood for most systems. In central China, soluble carbonate bedrock forms extensive karst landscapes. Current predictions are that the amount of monsoonal precipitation and acid rainfall in central China will increase, which is expected to lead to changes in the pH balance of karst ecosystems. To evaluate the role of pH, total organic carbon, and other geochemical parameters (e.g., Ca2+, Mg2+, NH4+, NOx, SO42-) in shaping bacterial communities within a single karst system in central China, samples were collected from the thin surface soils overlying Heshang Cave, cave sediments, and weathered cave passage rocks from the entrance, twilight, and dark zones, as well as from epikarstic drip waters inside the cave. Illumina sequencing of 16S rRNA genes and multivariate statistical analyses revealed that each tested community was distinct and the community variability was significantly correlated with pH, total organic carbon, and potassium concentrations. Specifically, surface soils were dominated by Acidobacteria, Verrucomicrobia and Planctomycetes, and diversity significantly decreased with acidic pH values. Nitrospirae, Gemmatimonadetes, Firmicutes, and Chloroflexi were unique to cave sediments, while Actinobacteria and Proteobacteria dominated weathered rocks and drip waters, respectively. The results reveal important implications regarding the effects of acidification on bacterial communities in karst areas, and on the control of pH in shaping bacterial communities throughout a karst system. Increased water flux into and through karst habitats due to monsoonal precipitation may result in deeper penetration of acidic solutions into karst and shift the bacterial communities inside the cave in the future.

Phylogenetic diversity of culturable fungi in the Heshang Cave, central China.

Caves are nutrient-limited and dark subterranean ecosystems. To date, attention has been focused on geological research of caves in China, whilst indigenous microbial diversity has been insufficiently characterized. Here, we report the fungal diversity in the pristine, oligotrophic, karst Heshang Cave, central China, using a culture-dependent method coupled with the analysis of the fungal rRNA-ITS gene sequences. A total of 194 isolates were obtained with six different media from 14 sampling sites of sediments, weathered rocks, and bat guanos. Phylogenetic analysis clustered the 194 sequenced isolates into 33 genera within 15 orders of three phyla, Ascomycota, Basidiomycota, and Zygomycota, indicating a high degree of fungal diversity in the Heshang Cave. Notably, 16 out of the 36 fungal genera were also frequently observed in solution caves around the world and 23 genera were previously found in carbonate cave, indicating potential similarities among fungal communities in cave ecosystems. However, 10 genera in this study were not reported previously in any solution caves, thus expanding our knowledge about fungal diversity in cave ecosystems. Moreover, culturable fungal diversity varied from one habitat to another within the cave, being the highest in sediments, followed by weathered rocks and bat guanos as indicated by α-diversity indexes. At the genus level, Penicillium accounted for 40, 54, and 52% in three habitats of sediments, weathered rocks, and bat guanos, respectively. Trichoderma, Paecilomyces, and Aspergillus accounted for 9, 22, and 37% in the above habitats, correspondingly. Despite of the dominance of Penicillium in all samples, ß-diversity index indicated significant differences between each two fungal communities in the three habitats in view of both the composition and abundance. Our study is the first report on fungal communities in a natural pristine solution cave system in central China and sheds light on fungal diversity and functions in cave ecosystems.