Identifying ecological processes driving vertical and horizontal archaeal community assemblages in a contaminated urban river

Effects of anthropogenic activities on the microbial community diversity of Ologe Lagoon sediment in Lagos State, Nigeria

The impact of pollution on the Ologe Lagoon was assessed by comparing physicochemical properties, hydrocarbon concentrations and microbial community structures of the sediments obtained from distinct sites of the lagoon. The locations were the human activity site (OLHAS), industrial-contaminated sites (OLICS) and relatively undisturbed site (OLPS). The physicochemical properties, heavy metal concentrations and hydrocarbon profiles were determined using standard methods. The microbial community structures of the sediments were determined using shotgun next-generation sequencing (NGS), taxonomic profiling was performed using centrifuge and statistical analysis was done using statistical analysis for metagenomics profile (STAMP) and Microsoft Excel. The result showed acidic pH across all sampling points, while the nitrogen content at OLPS was low (7.44 ± 0.085 mg/L) as compared with OLHAS (44.380 ± 0.962 mg/L) and OLICS (59.485 ± 0.827 mg/L). The levels of the cadmium, lead and nickel in the three sites were above the regulatory limits. The gas chromatography flame ionization detector (GC-FID) profile revealed hydrocarbon contaminations with nC14 tetradecane > alpha xylene > nC9 nonane > acenaphthylene more enriched at OLPS. Structurally, the sediments metagenomes consisted of 43 phyla,75 classes each, 165, 161, 166 orders, 986, 927 and 866 bacterial genera and 1476, 1129, 1327 species from OLHAS, OLICS and OLPS, respectively. The dominant phyla in the sediments were Proteobacteria, Firmicutes, Actinobacteria, and Chloroflexi. The principal component ordination (PCO) showed that OLPS microbial community had a total variance of 87.7% PCO1, setting it apart from OLHAS and OLICS. OLICS and OLHAS were separated by PCO2 accounting for 12.3% variation, and the most polluted site is the OLPS.

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.

Insights on the particle-attached riverine archaeal community shifts linked to seasons and to multipollution during a Mediterranean extreme storm event

Even if Archaea deliver important ecosystem services and are major players in global biogeochemical cycles, they remain poorly understood in freshwater ecosystems. To our knowledge, no studies specifically address the direct impact of xenobiotics on the riverine archaeome. Using environmental DNA metabarcoding of the 16S ribosomal gene, we previously demonstrated bacterial communities significant shifts linked to pollutant mixtures during an extreme flood in a typical Mediterranean coastal watercourse. Here, using the same methodology, we sought to determine whether archaeal community shifts coincided with the delivery of environmental stressors during the same flood. Further, we wanted to determine how archaea taxa compared at different seasons. In contrast to the bacteriome, the archaeome showed a specific community in summer compared to winter and autumn. We also identified a significant relationship between in situ archaeome shifts and changes in physicochemical parameters along the flood, but a less marked link to those parameters correlated to river hydrodynamics than bacteria. New urban-specific archaeal taxa significantly related to multiple stressors were identified. Through statistical modeling of both domains, our results demonstrate that Archaea, seldom considered as bioindicators of water quality, have the potential to improve monitoring methods of watersheds.

Multiple metal(loid) contamination reshaped the structure and function of soil archaeal community

Archaea are important participants in biogeochemical cycles of metal(loid)-polluted ecosystems, whereas archaeal structure and function in response to metal(loid) contamination remain poorly understood. Here, the effects of multiple metal(loid) pollution on the structure and function of archaeal communities were investigated in three zones within an abandoned sewage reservoir. We found that the high-contamination zone (Zone I) had higher archaeal diversity but a lower habitat niche breadth, relative to the mid-contamination zone (Zone II) and low-contamination zone (Zone III). Particularly, metal-resistant species represented by potential methanogens were markedly enriched in Zone I (cumulative relative abundance: 32.24%) compared to Zone II (1.93%) and Zone III (0.10%), and closer inter-taxon connections and higher network complexity (based on node number, edge number, and degree) were also observed compared to other zones. Meanwhile, the higher abundances of potential metal-resistant and methanogenic functions in Zone I (0.24% and 9.24%, respectively) than in Zone II (0.08% and 7.52%) and Zone III (0.01% and 1.03%) suggested archaeal functional adaptation to complex metal(loid) contamination. More importantly, six bioavailable metal(loid)s (titanium, tin, nickel, chromium, cobalt, and zinc) were the main contributors to archaeal community variations, and metal(loid) pollution reinforced the role of deterministic processes, particularly homogeneous selection, in the archaeal community assembly. Overall, this study provides the first integrated insight into the survival strategies of archaeal communities under multiple metal(loid) contamination, which will be of significant guidance for future bioremediation and environmental governance of metal(loid)-contaminated environments.

Knowledge Atlas on the Relationship between Water Management and Constructed Wetlands—A Bibliometric Analysis Based on CiteSpace

Water management is a crucial resource conservation challenge that mankind faces, and encouraging the creation of manmade wetlands with the goal of achieving long-term water management is the key to long-term urban development. To summarise and analyse the status of the research on the relationship between water management and constructed wetlands, this paper makes use of the advantages of the bibliometric visualization of CiteSpace to generate country/region maps and author-collaboration maps, and to analyse research hotspots and research dynamics by using keywords and literature co-citations based on 1248 pieces of related literature in the core collection in the Web of Science (WoS) database. The existing research shows that the research content and methods in the field of constructed-wetland and water-management research are constantly being enriched and deepened, including the research methods frequently used in constructed wetlands in water management and in the research content under concern, the functions and roles of constructed wetlands, the relevant measurement indicators of the purification impact of constructed wetlands on water bodies, and the types of water bodies treated by constructed wetlands in water management. We summarise the impact pathways of constructed wetlands on water management, as well as the impact factors of constructed wetlands under water-management objectives, by analysing the future concerns in the research field to provide references for research.

Per-, poly-fluoroalkyl substances (PFASs) and planktonic microbiomes: Identification of biotic and abiotic regulations in community coalescence and food webs

The importance of per-, poly-fluoroalkyl substances (PFASs) effects on riverine microbiomes is receiving increased recognition in the environmental sciences. However, few studies have explored how PFASs affect microbiomes across trophic levels, specifically through predator-prey interactions. This study examined the community profiles of planktonic archaea, bacteria, fungi, algae, protozoa, and metazoa in a semi-industrial and agricultural river alongside their interactions with 15 detected PFASs. As abiotic factors, PFASs affected community coalescence more than biogenic substances (p < 0.05). For biotic regulations, sub-communities in rare biospheres (including always rare taxa-ART and critically rare taxa-CRT) contributed to spatial community coalescence more than sub-communities in abundant biospheres (always abundant taxa-AAT and critically abundant taxa-CAT) (p < 0.05). Metazoa-bacteria (Modularity = 1.971) and protozoa-fungi (1.723) were determined to be the most stable predator-prey networks. Based on pathway models, short-chain PFBA (C4) was shown to weaken the trophic transfer efficiencies from heterotrophic bacteria (HB) to heterotrophic flagellates (HF) (p < 0.05). Long-chain PFTeDA (C14) promoted HB to amoeba (p < 0.05), which we postulate is the pathway for PFTeDA to enter the microbial food chain. Our preliminary results elucidated the influence of PFASs on planktonic microbial food webs and highlighted the need to consider protecting and remediating riverine ecosystems containing PFASs.

Hydrodynamic zones and the influence of microorganisms on nitrogen transformation in the diverging area of branched rivers

Diverging area is widespread in river networks, and understanding its biogeochemical process characteristics is of great significance to river ecological restoration and environmental quality improvement. Microbial communities affected by hydrodynamics play an important role in biogeochemical processes, but their relationship in diverging area is little known. Here, the composition of microbial community and its feedback to hydrodynamics and nitrogen conversion in the diverging area of river networks were first studied by coupling ecological theory, biogeochemical theory, microbial DNA sequencing and mathematical model of water environment. The results showed that there were five hydrodynamic zones with significant velocity differences in the diverging area, namely low velocity zone, maximum velocity zone, stagnant zone, separation zone, and deflection zone. According to the flow velocity grouping, there were significant differences in the microbial diversity and abundance among low velocity group, maximum velocity group and stagnant group had significant differences (p < 0.05, stress = 0.1207). In the low velocity group, Firmicutes was the dominant phylum which had a highest abundance and may promot the conversion of organic nitrogen into ammonia nitrogen. In the maximum velocity group, Bdellovibrionota was the dominant phylum which had a highest abundance and may promot the conversion of nitrate and nitric oxide to nitrogen. In the stagnant zone, Methylomirabilota was the dominant phylum which had a highest abundance and may promot the conversion of nitrogen into nitrate and ammonium. In addition, dissolved oxygen was the most sensitive environmental factor for shaping microorganisms and nitrogen conversion in the diverging area of the river networks by canonical correlation analysis. The denitrifying bacteria Rhodocyclaceae, was shown to negatively correlated with the flow velocity. This research improves the scientific basis for the study of the ecosystem in river networks, which will guide the construction of river ecological projects.

Different spatiotemporal dynamics, ecological drivers and assembly processes of bacterial, archaeal and fungal communities in brackish-saline groundwater

The presence of brackish-saline groundwater (BSG) poses great harms for human health, agricultural and industrial activity. Understanding how the major environmental features in BSG determine microbiota coalescence is crucial for groundwater monitoring optimization. Based on metabarcoding analysis of 242 PCR-amplified samples, we provided the first blueprints about distinct spatiotemporal distributions, ecological drivers and assembly processes of bacterial, archaeal and fungal communities in BSG obtained from new-constructed wells at Xiong'an New Area, China. Our study demonstrated that bacterial and archaeal communities exhibited significant spatial turnovers, while fungal community displayed the most obvious seasonal variation. Environmental filtering drove bacterial compositions more than those of archaea and fungi. Total dissolved solids (TDS), one of the most critical hydrochemical factors for salinization, had a stronger effect on bacterial spatiotemporal turnover than on those of the other two taxonomic groups, while chemical oxygen demand (CODMn) was more significantly associated with prokaryotic community variations. Bacterial and archaeal taxa dominated the metacommunity network and connected closely, and TDS was mostly related to archaeal subnetwork topological features, suggesting a significant influence of TDS on species association patterns within archaea. Specific functional guilds like bacterial nitrite oxidation, anammox, and archaeal methanogenesis were enriched in lower-TDS habitats, while higher TDS favored bacterial communities involved in dark oxidation of sulfur compounds, fumarate respiration, and cellulolysis. Finally, we confirmed that bacterial and archaeal assembly processes were governed by determinism in each season, and that of fungi was more regulated by stochasticity. Higher TDS was speculated to lead bacterial assembly more deterministic and that of fungi more random. Together, these findings provided an integrate theoretical framework about the unique responses of the three life domains to brackish-saline stress, and had important implications for microbial ecological prediction in groundwater.

Environmental factors and interactions among microorganisms drive microbial community succession during fermentation of Nongxiangxing daqu

Nongxiangxing daqu (daqu), which is produced by the open fermentation of wheat, is the fermentation starter of baijiu. This work reports the occurrence and driving factors of microbial community succession (MCS), which determines daqu quality, during daqu fermentation. The co-occurrence networks of the 2 stages of the MCS showed that module 2 of stage P1 contained Mucoromycota and Actinobacteriota and was affected by temperature, humidity, CO₂, and moisture; module 8 of stage P2 contained Mucoromycota and Saccharomycetes and was influenced by acidity and moisture. Twenty-two genera were thebiomarkers of the MCS. The MCS was driven by temperature, humidity, CO₂, O₂, acidity,moisture and interactions between the biomarkes and Lactobacillales, Saccharomycetales, and Acetobacter. The main driving factors of the bacterial community succession were acidity, moisture, and temperature, and that of the fungal community succession was moisture. These results guide the control of MCS during daqu fermentation.

Perfluorinated compounds (PFCs) in regional industrial rivers: Interactions between pollution flux and eukaryotic community phylosymbiosis

Perfluorinated compounds (PFCs) pose serious threats to aquatic ecosystems, especially their microbial communities. However, little is known about the phylosymbiosis of aquatic fungal and viridiplantae communities in response to PFC accumulation. We quantified the distribution of 14 PFCs in rivers and found that PFBA was dominant in the transition from water to sediment. High through-put sequencing revealed that phyla Ascomycota, Basidiomycota, Anthophyta, and Chlorophyta were the predominant in eukaryotic community. The effects of PFCs on spatial community coalescence at taxonomic and phylogenetic levels (p < 0.05) were revealed. Fungal community coalescence triggered the spatial assembly of fungal and viridiplantae communities in riverine environments (p < 0.05). Null modeling indicated that PFBA, PFTrDA and PFOS, etc, mediated phylogenetic assembly (p < 0.05) and stochastic processes (86.67-100%) maintain phylogenetic turnover in the fungal community. Meanwhile, variable selection (27.78-54.44%) explained the viridiplantae community assemblage. Finally, we identified fungal genera Hannaella, Naganishia, Purpureocillium and Stachybotrys as indicators for PFC pollution (p < 0.001). These results help explain the effects of PFCs on riverine ecological remediation.

Per-, poly-fluoroalkyl substances (PFASs) pollution in benthic riverine ecosystem: Integrating microbial community coalescence and biogeochemistry with sediment distribution

Per-, Poly-fluoroalkyl substances (PFASs) accumulation in benthic environments is mainly determined by material mixing and represents a significant challenge to river remediation. However, less attention has been paid to the effects of sediment distribution on PFASs accumulation, and how PFASs influence microbial community coalescence and biogeochemical processes. In order to identify correlations between PFASs distribution and benthic microbial community functions, we conducted a field study and quantified the ecological constrains of material transportation on benthic microorganisms. Perfluorohexanoic acid (PFHxA) contributed most to the taxonomic heterogeneity of both archaeal (12.199%) and bacterial (13.675%) communities. Genera Methanoregula (R² = 0.292) and Bacillus (R² = 0.791) were identified as indicators that respond to PFASs. Phylogenetic null modeling indicated that deterministic processes (50.0-82.2%) dominated in spatial assembly of archaea, while stochasticity (94.4-97.8%) dominated in bacteria. Furthermore, spatial mixing of PFASs influenced broadly in nitrogen cycling of archaeal genomes, and phosphorus mineralization of bacterial genomes (p < 0.05). Overall, we quantified the effect of PFASs on community assembly and highlighted the constrains of PFASs influence on benthic geochemical potentials, which may provide new insights into riverine remediation.

Planktonic microbial responses to perfluorinated compound (PFC) pollution: Integrating PFC distributions with community coalescence and metabolism

The presence of perfluorinated compound (PFC) contamination in riverine ecosystems represents a novel challenge for environmental remediation. However, little attention has been paid to how PFCs affect planktonic microbial community coalescence. Here, the spatial profiles of fourteen PFCs and their contributions to community assembly were determined using field sampling in a natural river confluence. Overall, PFPeA (perfluorovaleric acid), PFBS (perfluorobutylsulfonate), PFHpA (perfluoroheptanoic acid) and PFHxA (perfluorohexanoic acid) were identified as important indicators of PFC pollution, accounting for the majority of the spatial heterogeneity in PFC pollution. PFPeA (perfluorovaleric acid) (9.39%) and PFTrDA (perfluorotridecanoate acid) (8.61%) contributed more to microbial taxonomic spatial heterogeneity than did other factors, such as pH, dissolved oxygen and velocity. PFOA (pentadecafluorooctanoic acid) (R² = 0.353) and PFBS (R² = 0.297) drove turnover in archaeal communities within river sections (transversely), while PFHpA (R² = 0.251) and PFOS (perfluorooctane sulphonate) (R² = 0.105) drove turnover in bacterial communities transversely and longitudinally, respectively. Phylogenetic null modeling suggested that archaeal (68.89-83.33%) community assembly was dominated by stochastic processes, and was balanced by PFHxA (R² = 0.349) and PFOA (R² = 0.290). Furthermore, PFOS inhibited the biosynthesis of several key amino acids in archaea, and PFBA enhanced the potential for bacterial infections in humans (p < 0.05), threatening water quality. In sum, this study provides new insights into riverine ecological risk management.

Water flow and temperature drove epiphytic microbial community shift: Insight into nutrient removal in constructed wetlands from microbial assemblage and co-occurrence patterns

The impacts of water flow and low temperature on nutrient removal and underlying ecological mechanism of epiphytic microbial community in constructed wetlands remain to be fully illustrated. In this study, low temperature inhibited the decrease of TN, NH₄⁺-N, TP, and COD concentrations in water, but water flow decreased NH₄⁺-N and COD concentrations strikingly. The relative conductivity, soluble sugar, and protein of M. spicatum increased, while the total chlorophyll contents decreased significantly under the stress of water flow and low temperature. Temperature affected the alpha-diversity and composition of the microbial community, while water flow caused differences in community distribution. Deterministic processes dominated in microbial community assembly with increasing environmental stress. Co-occurrence network analysis demonstrated that Chlorophyta, Verrucomicrobia, Proteobacteria, Bacteroidetes, and Firmicutes phyla were the dominant hubs in September, however, low temperatures caused a shift to Metazoan dominated network, demonstrating diminished nutrient removal capacity.

The response of microbial community structure and sediment properties to anthropogenic activities in Caohai wetland sediments

This study aimed to investigate the response of sediment microbial communities (including bacteria and archaeal groups) in Caohai Lake to anthropogenic activities. The sediment samples were collected from the regions with high anthropogenic interference and low anthropogenic interference. Their physicochemical properties and enzyme activities were analyzed, and the bacterial and archaeal communities were investigated using high-throughput sequencing technology. The results showed that the physicochemical characters changed by anthropogenic activities were the important factors that influenced enzyme activities, alpha diversity, key functional taxa, and community structure. And the impact of anthropogenic activities on microbial communities might follow a non-linear pattern. Furthermore, few significant differences of alpha indices between the high and low disturbed areas, but clear differences of microbial community composition analysis and beta-diversity analysis were observed. The hypothesis was proved that the intensity of anthropogenic impacts in Caohai had not reached the potential thresholds. The best distinguish biomarkers between the two areas and the most related key nodes among the network did not always have a high microbial abundance. The anthropogenic activities might influence the microbial community by affecting a small number of the key taxon in the ecological network. These findings provided a valuable understanding of how sediment microorganisms respond to anthropogenic activities in Caohai Lake.