Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism.

Autism spectrum disorder (ASD) is a complex developmental syndrome of unknown etiology. Recent studies employing exome- and genome-wide sequencing have identified nine high-confidence ASD (hcASD) genes. Working from the hypothesis that ASD-associated mutations in these biologically pleiotropic genes will disrupt intersecting developmental processes to contribute to a common phenotype, we have attempted to identify time periods, brain regions, and cell types in which these genes converge. We have constructed coexpression networks based on the hcASD "seed" genes, leveraging a rich expression data set encompassing multiple human brain regions across human development and into adulthood. By assessing enrichment of an independent set of probable ASD (pASD) genes, derived from the same sequencing studies, we demonstrate a key point of convergence in midfetal layer 5/6 cortical projection neurons. This approach informs when, where, and in what cell types mutations in these specific genes may be productively studied to clarify ASD pathophysiology.

Environmental DNA metabarcoding reveals the impacts of anthropogenic pollution on multitrophic aquatic communities across an urban river of western China.

Anthropogenic activities are intensively affecting the structure and function of biological communities in river ecosystems. The effects of anthropogenic pollution on single-trophic community have been widely explored, but their effects on the structures and co-occurrence patterns of multitrophic communities remain largely unknown. In this study, we collected 13 water samples from the Neijiang River in Chengdu City of China, and identified totally 2352 bacterial, 207 algal, 204 macroinvertebrate, and 33 fish species based on the eDNA metabarcoding to systematically investigate the responses of multitrophic communities to environmental stressors. We observed significant variations in bacterial, algal, and macroinvertebrate community structures (except fish) with the pollution levels in the river. Network analyses indicated a more intensive interspecific co-occurrence pattern at high pollution level. Although taxonomic diversity of the multitrophic communities varied insignificantly, phylogenetic diversities of fish and algae showed significantly positive and negative associations with the pollution levels, respectively. We demonstrated the primary role of environmental filtering in driving the structures of bacteria, algae, and macroinvertebrates, while the fish was more controlled by dispersal limitation. Nitrogen was identified as the most important factor impacting the multitrophic community, where bacterial composition was mostly associated with NO3--N, algal spatial differentiation with TN, and macroinvertebrate and fish with NH4+-N. Further partial least-squares path model confirmed more important effect of environmental variables on the relative abundance of bacteria and algae, while macroinvertebrate and fish communities were directly driven by the algae-mediated pathway in the food web. Our study highlighted the necessity of integrated consideration of multitrophic biodiversity for riverine pollution management, and emphasized the importance of controlling nitrogen inputs targeting a healthy ecosystem.

Occurrence, distribution and risk assessment of polycyclic aromatic hydrocarbons in soils around main water source areas of Beijing, China.

Polycyclic aromatic hydrocarbons (PAHs) in urban environments have been globally concerned due to their significant health impacts on residents. However, little is known about potential risks of PAHs from centralized water source areas. In the present study, 326 soils samples from the main water source areas of Beijing were collected and the occurrence, source appointment, and risks of PAHs were systematically investigated based on the monitoring results from high-performance liquid chromatography (HPLC). The total PAHs (∑16 PAHs) concentrations ranged from 5.70 to 1512 ng/g with median value of 44.2 ng/g, in which 4-ring and 5-ring groups were the major components. PAHs concentrations in the cultivated land were significantly higher than other areas, which could reflect significant impact of soil organic matter and total nitrogen contents on the spatial variations of PAHs. Further source identifications through positive matrix factorization model (PMF) revealed that biomass (22.5%), coal (21.4%), gasoline (17.6%) and diesel (16.4%) combustion were dominant sources of soil PAHs in the study area. Moreover, the risk assessment indicated that total ecological and health risk of PAHs were negligible, but individual PAH, including pyrene and benzo(b)fluoranthene, should be concerned due to their potential risks in several monitored stations located in the secondary protection area of four reservoirs. Our study provided new insights into environmental risks of soils in main water source areas from PAHs and could be helpful for organic micropollutant controlling and drinking water safety in rapidly urbanizing cities.

Impacts of engineered nanoparticles and antibiotics on denitrification: Element cycling functional genes and antibiotic resistance genes.

The wide presence of antibiotics and minerals warrants their combined effects on the denitrification in natural aquatic environment. Herein, we investigated the effects of two antibiotics, sulfamethazine (SMZ) and chlortetracycline (CTC), on the reduction of NO3--N and accumulation of NO2--N in the absence and presence of engineered nanoparticles (NPs) (Al2O3, SiO2, and geothite) using 16 S rRNA sequencing and high-throughput quantitative PCR. The results showed that the addition of antibiotics inhibited the reduction of NO3--N by changing the bacterial community structure and reducing the abundance of denitrification genes, while engineered NPs promoted the denitrification by increasing the abundance of denitrification genes. In the binary systems, engineered NPs alleviated the inhibitory effect of antibiotics through enriching the denitrification genes and adsorbing antibiotics. Antibiotics and its combination with engineered NPs changed the composition of functional genes related to C, N, P, S metabolisms (p < 0.01). The addition of antibiotics and/or engineered NPs altered the bacterial community structure, which is dominated by the genera of Enterobacter (40.7-90.5%), Bacillus (4.9-58.5%), and Pseudomonas (0.21-12.7%). The significant relationship between denitrification, carbon metabolism genes, and antibiotic resistance genes revealed that the heterotrophic denitrifying bacteria may host the antibiotic resistance genes and denitrification genes simultaneously. The findings underscore the significance of engineered NPs in the toxicity assessment of pollutants, and provide a more realistic insight into the toxicity of antibiotics in the natural aquatic environment.

Colonisation of Oncidium orchid roots by the endophyte Piriformospora indica restricts Erwinia chrysanthemi infection, stimulates accumulation of NBS-LRR resistance gene transcripts and represses their targeting micro-RNAs in leaves.

BACKGROUND: Erwinia chrysanthemi (Ec) is a destructive pathogen which causes soft-rot diseases in diverse plant species including orchids. We investigated whether colonization of Oncidium roots by the endophytic fungus Piriformospora indica (Pi) restricts Ec-induced disease development in leaves, and whether this might be related to the regulation of nucleotide binding site-leucine rich repeat (NBS-LRR) Resistance (R) genes. RESULTS: Root colonization of Oncidium stackings by Pi restricts progression of Ec-induced disease development in the leaves. Since Pi does not inhibit Ec growth on agar plates, we tested whether NBS-LRR R gene transcripts and the levels of their potential target miRNAs in Oncidium leaves might be regulated by Pi. Using bioinformatic tools, we first identified NBS-LRR R gene sequences from Oncidium, which are predicted to be targets of miRNAs. Among them, the expression of two R genes was repressed and the accumulation of several regulatory miRNA stimulated by Ec in the leaves of Oncidium plants. This correlated with the progression of disease development, jasmonic and salicylic acid accumulation, ethylene synthesis and H2O2 production after Ec infection of Oncidium leaves. Interestingly, root colonization by Pi restricted disease development in the leaves, and this was accompanied by higher expression levels of several defense-related R genes and lower expression level of their target miRNA. CONCLUSION: Based on these data we propose that Pi controls the levels of NBS-LRR R mRNAs and their target miRNAs in leaves. This regulatory circuit correlates with the protection of Oncidium plants against Ec infection, and molecular and biochemical investigations will demonstrate in the future whether, and if so, to what extent these two observations are related to each other.

Growth promotion and disease resistance induced in Anthurium colonized by the beneficial root endophyte Piriformospora indica.

BACKGROUND: Anthurium andraeanum, an important ornamental flower, has to go through a growth-delaying period after transfer from tissue culture to soil, which requires time and extra costs. Furthermore, during this period, the plantlets are highly susceptible to bacterial infections, which results in impaired development and severe losses. Here, we aimed to address whether application of the endophytic fungus, Piriformospora indica protects the A. andraeanum root system during the critical propagation period, and whether P. indica reduce the mortality rate by stimulating the host's resistance against diseases. RESULTS: We demonstrate that P. indica shortens the recovery period of Anthurium, promotes growth and confers disease resistance. The beneficial effect of P. indica results in faster elongation of Anthurium roots early in the interaction. P. indica-colonized plants absorb more phosphorus and exhibit higher photosynthesis rates than uncolonized control plants. Moreover, higher activities of stress-related enzymes, of jasmonic acid levels and mRNA levels of jasmonic acid-responsive genes suggest that the fungus prepares the plant to respond more efficiently to potentially upcoming threats, including bacterial wilt. CONCLUSION: These results suggest that P. indica is a helpful symbiont for promoting Anthurium rooting and development. All our evidences are sufficient to support the disease resistance conferred by P. indica through the plant-fungal symbiosis. Furthermore, it implicates that P. indica has strong potential as bio-fertilizer for utilization in ornamental plant cultivation.

Simultaneous dimension reduction and adjustment for confounding variation.

Dimension reduction methods are commonly applied to high-throughput biological datasets. However, the results can be hindered by confounding factors, either biological or technical in origin. In this study, we extend principal component analysis (PCA) to propose AC-PCA for simultaneous dimension reduction and adjustment for confounding (AC) variation. We show that AC-PCA can adjust for (i) variations across individual donors present in a human brain exon array dataset and (ii) variations of different species in a model organism ENCODE RNA sequencing dataset. Our approach is able to recover the anatomical structure of neocortical regions and to capture the shared variation among species during embryonic development. For gene selection purposes, we extend AC-PCA with sparsity constraints and propose and implement an efficient algorithm. The methods developed in this paper can also be applied to more general settings. The R package and MATLAB source code are available at https://github.com/linzx06/AC-PCA.

Spatio-temporal transcriptome of the human brain.

Brain development and function depend on the precise regulation of gene expression. However, our understanding of the complexity and dynamics of the transcriptome of the human brain is incomplete. Here we report the generation and analysis of exon-level transcriptome and associated genotyping data, representing males and females of different ethnicities, from multiple brain regions and neocortical areas of developing and adult post-mortem human brains. We found that 86 per cent of the genes analysed were expressed, and that 90 per cent of these were differentially regulated at the whole-transcript or exon level across brain regions and/or time. The majority of these spatio-temporal differences were detected before birth, with subsequent increases in the similarity among regional transcriptomes. The transcriptome is organized into distinct co-expression networks, and shows sex-biased gene expression and exon usage. We also profiled trajectories of genes associated with neurobiological categories and diseases, and identified associations between single nucleotide polymorphisms and gene expression. This study provides a comprehensive data set on the human brain transcriptome and insights into the transcriptional foundations of human neurodevelopment.

Coupling diffusion imaging with histological and gene expression analysis to examine the dynamics of cortical areas across the fetal period of human brain development.

As a prominent component of the human fetal brain, the structure of the cerebral wall is characterized by its laminar organization which includes the radial glial scaffold during fetal development. Diffusion tensor imaging (DTI) is useful to quantitatively delineate the microstructure of the developing brain and to clearly identify transient fetal layers in the cerebral wall. In our study, the spatio-temporal microstructural changes in the developing human fetal cerebral wall were quantitatively characterized with high-resolution DTI data of postmortem fetal brains from 13 to 21 gestational weeks. Eleven regions of interest for each layer in the entire cerebral wall were included. Distinctive time courses of microstructural changes were revealed for 11 regions of the neocortical plate. A histological analysis was also integrated to elucidate the relationship between DTI fractional anisotropy (FA) and histology. High FA values correlated with organized radial architecture in histological image. Expression levels of 17565 genes were quantified for each of 11 regions of human fetal neocortex from 13 to 21 gestational weeks to identify transcripts showing significant correlation with FA change. These correlations suggest that the heterogeneous and regionally specific microstructural changes of the human neocortex are related to different gene expression patterns.

TBR1 directly represses Fezf2 to control the laminar origin and development of the corticospinal tract.

The corticospinal (CS) tract is involved in controlling discrete voluntary skilled movements in mammals. The CS tract arises exclusively from layer (L) 5 projection neurons of the cerebral cortex, and its formation requires L5 activity of Fezf2 (Fezl, Zfp312). How this L5-specific pattern of Fezf2 expression and CS axonal connectivity is established with such remarkable fidelity had remained elusive. Here we show that the transcription factor TBR1 directly binds the Fezf2 locus and represses its activity in L6 corticothalamic projection neurons to restrict the origin of the CS tract to L5. In Tbr1 null mutants, CS axons ectopically originate from L6 neurons in a Fezf2-dependent manner. Consistently, misexpression of Tbr1 in L5 CS neurons suppresses Fezf2 expression and effectively abolishes the CS tract. Taken together, our findings show that TBR1 is a direct transcriptional repressor of Fezf2 and a negative regulator of CS tract formation that restricts the laminar origin of CS axons specifically to L5.

Occurrence, mass loading, and post-control temporal trend of legacy perfluoroalkyl substances (PFASs) in the middle and lower Yangtze River.

Present study focused on per- and polyfluoroalkyl substances (PFASs) occurrence in dry and wet seasons in the middle and lower Yangtze River (YZR) and changing temporal trends after years of control. Results revealed that perfluorooctanoic acid (PFOA) was 75 % of total PFAS concentrations (∑11PFASs). ∑11PFASs were ranged 0.20-28.49 ng/L and 1.17-112.84 µg/kg in water and sediment. The logKoc of perfluoroalkyl carboxylic acids was positive with the carbon chain length (p < 0.05, r2 = 0.78). A meta-analysis of results from 16 peer-reviewed publications about PFASs in the YZR showed that fluorochemical industries strongly influenced the high PFAS levels in the detected scenes. PFOA was still the primary pollutant. Individual PFAS in the lower reach was higher than those in the middle reach. The mass loading of PFASs imported into the sea was 10.80 t/y. This study will help develop effective approaches for controlling emerging pollutants in the YZR.

Distribution and drivers of co-hosts of antibiotic and metal(loid) resistance genes in the fresh-brackish-saline groundwater.

Groundwater is an essential source of drinking water and agricultural irrigation water, and its protection has become a global goal for public health. However, knowledge about heavy metal(loid) resistance genes (MRGs) in groundwater and the potential co-selection of antibiotic resistance genes (ARGs) have seldom been developed. Here, during the wet and dry seasons, we collected 66 groundwater samples (total dissolved solids = 93.9-9530 mg/L) adjacent to Baiyangdian Lake in Northern China, which presented the few metal(loid) and antibiotic contamination. We identified 160 MRGs whose composition exhibited significant seasonal variation, and dissolved metal(loid)s (particularly Ba) played a determinative role in promoting the MRGs proliferation though with relatively low concentrations, suggesting the relatively vulnerable groundwater ecosystems. Moreover, 27.4% of MRG-carrying metagenome-assembled genomes (MAGs) simultaneously carried ARGs, with the most frequently detected MRG types of Cu, Hg, and As, and ARG types of multidrug and bacitracin. Physicochemical variables, variables related to total dissolved solids, metal(loid)s, and antibiotics synthetically shaped the variation of MRG-ARG hosts in groundwater. We found that the increase of MRG-ARG hosts was critically responsible for the spread of MRGs and ARGs in groundwater. Our findings revealed the widespread co-occurrence of MRGs and ARGs in few-contaminated groundwater and highlighted the crucial roles of salinity in their propagation and transmission.

A mixed blessing of influent leachate microbes in downstream biotreatment systems of a full-scale landfill leachate treatment plant.

In landfill leachate treatment plants (LLTPs), the microbiome plays a pivotal role in the decomposition of organic compounds, reduction in nutrient levels, and elimination of toxins. However, the effects of microbes in landfill leachate influents on downstream treatment systems remain poorly understood. To address this knowledge gap, we collected 23 metagenomic and 12 metatranscriptomic samples from landfill leachate and activated sludge from various treatment units in a full-scale LLTP. We successfully recovered 1,152 non-redundant metagenome-assembled genomes (MAGs), encompassing a wide taxonomic range, including 48 phyla, 95 classes, 166 orders, 247 families, 238 genera, and 1,152 species. More diverse microbes were observed in the influent leachate than in the downstream biotreatment systems, among which, an unprecedented ∼30 % of microbes with transcriptional expression migrated from the influent to the biological treatment units. Network analysis revealed that 399 shared MAGs across the four units exhibited high node centrality and degree, thus supporting enhanced interactions and increased stability of microbial communities. Functional reconstruction and genome characterization of MAGs indicated that these shared MAGs possessed greater capabilities for carbon, nitrogen, sulfur, and arsenic metabolism compared to non-shared MAGs. We further identified a novel species of Zixibacteria in the leachate influent with discrete lineages from those in other environments that accounted for up to 17 % of the abundance of the shared microbial community and exhibited notable metabolic versatility. Meanwhile, we presented groundbreaking evidence of the involvement of Zixibacteria-encoded genes in the production of harmful gas emissions, such as N2O and H2S, at the transcriptional level, thus suggesting that influent microbes may pose safety risks to downstream treatment systems. In summary, this study revealed the complex impact of the influent microbiome on LLTP and emphasizes the need to consider these microbial characteristics when designing treatment technologies and strategies for landfill leachate management.

[Numerical analysis of morphological variation of germplasm resources of dioscorea].

OBJECTIVE: Botanical characters of germplasm resources of Dioscorea were observed and compared, which could to offer reference for its genetic improvement, germplasm resource identification and classification. METHOD: Based on field cultivation, twenty-four morphological traits of ninety-four Dioscorea germplasm resources were observed or determined. And the morphological differences among germplasm resources were compared by principal component analysis and cluster analysis. RESULT: There were ample morphological diversity in the twenty-four traits, in especially in leaf size and tuber characters of the ninety-four Dioscorea germplasm resources. The first seven principal components which accounted for 80. 957% of total variance were extracted from the principal component analysis. The ninety-four germplasm resources could be divided into four clusters, which belonging to Dioscorea opposite, D. persimili, D. fordii and D. alata respectively. CONCLUSION: There were large morphological variation among germplasm resources on Dioscorea. Identification of germplasm resources of Dioscorea should focus on leaf size and tuber characters.

Bioaccumulation of pharmaceuticals and personal care products (PPCPs) in freshwater pearl mussels Hyriopsis cumingii in Poyang Lake.

Thirty-five PPCPs were measured in representative freshwater pearl mussels (Hyriopsis cumingii) in Poyang Lake, the largest lake of China, as well as their responses to sedimentary PPCPs. We observed 32 PPCPs in soft tissues of mussels at a total concentration of 2721.5 ± 929.3 ng·g-1 dry weight (dw), much higher than those in sediments (21 PPCPs, 273.2 ± 89.4 ng·g-1 dw). Anti-inflammatories were the primary contaminants detected in both sediments and mussels. PPCP concentrations in mussels exhibited significant organ-specific characteristics, and gonads were identified as a hotspot for these contaminants. Correlation analysis showed that gonads were more likely to assimilate triclosan from sediments. Biochemical analysis revealed a higher physiological sensitivity of glutathione synthesis in gonads to sedimentary PPCPs, suggesting the long-term oxidative damage. Our findings highlight the concern on the potential effects of sedimentary PPCPs to propagation of mussels, and emphasize the necessity to formulate strategies for sedimentary PPCPs control targeting a healthy lake.

Antibiotic profiles and their relationships with multitrophic aquatic communities in an urban river.

Antibiotics have garnered worldwide attention due to their omnipresence and detrimental effects on aquatic organisms, yet their potential relationships with multitrophic aquatic communities in natural rivers remain largely unknown. Here, we examined 107 antibiotics in water and sediment from an urban river in Chengdu, Sichuan province (China). The bacterial, algal, macroinvertebrates, and fish communities were synchronously measured based on the environmental DNA (eDNA) metabarcoding approach, and their relationships with antibiotics were further investigated. The results showed that the total antibiotic concentrations ranged from 1.12 to 377 ng/L and from 7.95 to 145 ng/g in water and sediment, respectively. Significant seasonal variations in the concentrations and compositions of antibiotics in water were observed. eDNA metabarcoding revealed great compositional variations of bacterial, algal, macroinvertebrates, and fish communities along the river, and antibiotics had significant negative relationships with the community diversities of aquatic organisms (p < 0.05) except for fish. Meanwhile, significant negative correlations were observed between antibiotic concentrations and the relative abundances of essential metabolism pathways of bacteria, e.g., energy metabolism (p < 0.05), carbohydrate metabolism (p < 0.05), and lipid metabolism (p < 0.01). Moreover, antibiotics demonstrated greater effects on the function of bacterial community compared with environmental variables. The findings highlight the significance of eDNA metabarcoding approach in revealing the relationships between aquatic communities and antibiotics, and call for further studies on the effects of antibiotics on multitrophic aquatic communities in natural waters.

Ecological differentiation and assembly processes of abundant and rare bacterial subcommunities in karst groundwater.

The ecological health of karst groundwater has been of global concern due to increasing anthropogenic activities. Bacteria comprising a few abundant taxa (AT) and plentiful rare taxa (RT) play essential roles in maintaining ecosystem stability, yet limited information is known about their ecological differentiation and assembly processes in karst groundwater. Based on a metabarcoding analysis of 64 groundwater samples from typical karst regions in southwest China, we revealed the environmental drivers, ecological roles, and assembly mechanisms of abundant and rare bacterial communities. We found a relatively high abundance of potential functional groups associated with parasites and pathogens in karst groundwater, which might be linked to the frequent regional anthropogenic activities. Our study confirmed that AT was dominated by Proteobacteria and Campilobacterota, while Patescibacteria and Chloroflexi flourished more in the RT subcommunity. The node-level topological features of the co-occurrence network indicated that AT might share similar niches and play more important roles in maintaining bacterial community stability. RT in karst groundwater was less environmentally constrained and showed a wider environmental threshold response to various environmental factors than AT. Deterministic processes, especially homogeneous selection, tended to be more important in the community assembly of AT, whereas the community assembly of RT was mainly controlled by stochastic processes. This study expanded our knowledge of the karst groundwater microbiome and was of great significance to the assessment of ecological stability and drinking water safety in karst regions.

Structure, stability, and potential function of groundwater microbial community responses to permafrost degradation on varying permafrost of the Qinghai-Tibet Plateau.

The ongoing permafrost degradation under climate warming has modified aboveground biogeochemical processes mediated by microbes, yet groundwater microbial structure and function as well as their response to permafrost degradation remain poorly understood. We separately collect 20 and 22 sub-permafrost groundwater samples from Qilian Mountain (alpine and seasonal permafrost) and Southern Tibet Valley (plateau isolated permafrost) on the Qinghai-Tibet Plateau (QTP) to investigate the effects of permafrost groundwater characteristics on the diversity, structure, stability, and potential function of bacterial and fungal communities. Regional discrepancy of groundwater microbes between two permafrost regions reveals that permafrost degradation might reshape microbial community structure, increase community stability and potential functions relevant to carbon metabolism. Bacterial community assembly in permafrost groundwater is governed by deterministic processes, whereas fungal communities are mainly controlled by stochastic processes, suggesting that bacterial biomarkers might provide the better 'early warning signals' to permafrost degradation in deeper layers. Our study highlights the importance of groundwater microbes in ecological stability and carbon emission on the QTP.

Metagenomic analysis unveils the underexplored roles of prokaryotic viruses in a full-scale landfill leachate treatment plant.

Enormous viral populations have been identified in activated sludge systems, but their ecological and biochemical roles in landfill leachate treatment plants remain poorly understood. To address this knowledge gap, we conducted an in-depth analysis using 36 metagenomic datasets that we collected and sequenced during a half-year time-series sampling campaign at six sites in a full-scale landfill leachate treatment plant (LLTP), elucidating viral distribution, virus‒host dynamics, virus-encoded auxiliary metabolic genes (AMGs), and viral contributions to the spread of virulence and antibiotic resistance genes. Our findings demonstrated that viral and prokaryotic communities differed widely among different treatment units, with stability over time. LLTP viruses were linked to various prokaryotic hosts, spanning 35 bacterial phyla and one archaeal phylum, which included the core microbes involved in biological treatments, as well as some of the less well-characterized microbial dark matter phyla. By encoding 2364 auxiliary metabolic genes (AMGs), viruses harbored the potential to regulate microbial nucleotide metabolism, facilitate the biodegradation of complex organic matter, and enhance flocculation and settling in biological treatment plants. The abundance distribution of AMGs varied considerably across treatment units and showed a lifestyle-dependent pattern with temperate virus-associated AMGs exhibiting a higher average abundance in downstream biological treatment units and effluent water. Meanwhile, temperate viruses tended to carry a higher load of virulence factor genes (VFGs), antibiotic resistance genes (ARGs), and biotic and metal resistance genes (BMRGs), and engaged in more frequent gene exchanges with prokaryotes than lytic viruses, thus acting as a pivotal contributor to the dissemination of pathogenicity and resistance genes in downstream LLTP units. This study provided a comprehensive profile of viral and prokaryotic communities in the LLTP and unveiled the varying roles of different-lifestyle viruses in biochemical processes and water quality safety.

Planktonic/benthic Bathyarchaeota as a "gatekeeper" enhance archaeal nonrandom co-existence and deterministic assembling in the Yangtze River.

Archaea, the third proposed domain of life, mediate carbon and nutrient cycling in global natural habitats. Compared with bacteria, our knowledge about archaeal ecological modes in large freshwater environments subject to varying natural and human factors is limited. By metabarcoding analysis of 303 samples, we provided the first integrate biogeography about archaeal compositions, co-existence networks, and assembling processes within a 6000 km continuum of the Yangtze River. Our study revealed that, among the major phyla, water samples owned a higher proportion of Thaumarchaeota (62.8%), while sediments had higher proportions of Euryarchaeota (33.4%) and Bathyarchaeota (18.8%). A decline of polarization in phylum abundance profile was observed from plateau/mountain/hill to basin/plain areas, which was attributed to the increase of nutrients and metals. Planktonic and benthic Bathyarchaeota tended to co-occur with both major (e.g., methanogens or Thermoplasmata) and minor (e.g., Asgard or DPANN) taxa in the non-random networks, harboring the highest richness and abundances of keystone species and contributing the most positively to edge number, node degree, and nearest neighbor degree. Furthermore, we noted significantly positive contributions of Bathyarchaeota abundance and network complexity to the dominance of deterministic process in archaeal assembly (water: 65.3%; sediments: 92.6%), since higher carbon metabolic versatility of Bathyarchaeota would benefit archaeal symbiotic relations. Stronger deterministic assembling was identified at the lower-reach plain, and higher concentrations of ammonium and aluminum separately functioning as nutrition and agglomerator were the main environmental drivers. We lastly found that the Three Gorges Dam caused a simultaneous drop of benthic Bathyarchaeota abundance, network co-existence, and deterministic effects immediately downstream due to riverbed erosion as a local interference. These findings highlight that Bathyarchaeota are a "gatekeeper" to promote fluvial archaeal diversity, stability, and predictability under varying macroscopic and microscopic factors, expanding our knowledge about microbial ecology in freshwater biogeochemical cycling globally.