Influences of plant type on bacterial and archaeal communities in constructed wetland treating polluted river water

DNA metabarcoding reveals ecological patterns and driving mechanisms of archaeal, bacterial, and eukaryotic communities in sediments of the Sansha Yongle Blue Hole

The Sansha Yongle Blue Hole (SYBH) is the world's deepest marine blue hole with unique physicochemical characteristics. However, our knowledge of the biodiversity and community structure in SYBH sediments remains limited, as past studies have mostly focused on microbial communities in the water column. Here, we collected sediment samples from the aerobic zone (3.1 to 38.6 m) and the deep anaerobic zone (150 m, 300 m) of the SYBH and extracted DNA to characterize the archaeal, bacterial, and eukaryotic communities inhabiting these sediments. Our results showed that the archaeal and bacterial communities were dominated by Thaumarchaeota and Proteobacteria, respectively. The dominant taxa of eukaryotes in different sites varied greatly, mainly including Phaeophyceae, Annelida, Diatomea and Arthropoda. All three examined domains showed clear vertical distributions and significant differences in community composition between the aerobic and anaerobic zones. Sulfide played a prominent role in structuring the three domains, followed by salinity, nitrous oxide, pH, temperature and dissolved oxygen, all of which were positively correlated with the turnover component, the main contributor to beta diversity. Neutral community model revealed that stochastic processes contributed to more than half of the community variations across the three domains. Co-occurrence network showed an equal number of positive and negative interactions in the archaeal network, while positive interactions accounted for ~ 80% in the bacterial and eukaryotic networks. Our findings reveal the ecological features of prokaryotes and eukaryotes in SYBH sediments and shed new light on community dynamics and survival strategies in the special environment of marine blue holes.

Both species richness and growth forms affect nutrient removal in constructed wetlands: A mesocosm experiment

Introduction

Plant richness is thought to improve the function of constructed wetlands (CWs), but most CWs are planted with monocultures, with only a few employed polycultures, which have drawn contradictory conclusions. We suppose functional diversity is the key to better performance of plant communities and hypothesize that CWs planted with diverse growth forms are superior in plant growth and nutrient removal.

Methods

In this study, six emergent plant species categorized into slender type (Schoenoplectus tabernaemontani, Typha orientalis), fan type (Iris sibirica, Acorus calamus) and large type (Canna indica and Thalia dealbata) were planted in monocultures, combinations (two species of the same growth form) and mixed polycultures (six species of three growth forms). We then compared how plant growth and nutrient uptake differed among treatments.

Results

It showed that the polyculture considerably increased the removal of total nitrogen (TN) and total phosphorus (TP), but the combination did not outperform monoculture. High consistency in the patterns between underground biomass and total biomass indicated that plant roots were essential for nutrient consumption. Compared with slender and fan plants, the large plants had a greater biomass increase in polycultures, which greatly accelerated the absorption and assimilation of TN and TP.

Conclusion

Our study indicated that plant community with various growth forms reduced the intensity of interspecific competition, increased the functional diversity, and greatly enhanced the ability of pollutant removal. Our results also provide some suggestions for plant selection and combination designs in CWs.

The Interaction Effects of Aeration and Plant on the Purification Performance of Horizontal Subsurface Flow Constructed Wetland

Aeration and plants exhibit influence on the water purification performance in constructed wetlands (CWs). However, the interaction between aeration and plants on enhancing performance of domestic sewage treatment is unclear. Our study aims to optimize the combination of aeration position and plant species, promoting the extensive and effective application of CWs. Herein, six horizontal subsurface flow (HSSF) CWs small scale plots were established and divided into two groups according to the plant (i.e., Canna indica and Iris sibirica). To adjust the distribution of dissolved oxygen (DO) in CWs, each group had three plots of HSSF CWs. One plot was aerated at the bottom of the first quarter of the filtration chamber, one plot was aerated at the bottom of the inflow chamber, and the remaining plot was not aerated as a control. Results showed that aeration at the bottom of the first quarter filtration chamber could contribute to the highest removal efficiency of chemical oxygen demand (COD), ammonium nitrogen (NH4+-N) and total nitrogen (TN). The COD, NH4+-N, and TN removal percentages decreased with the drop in temperature. However, the plot aerated at the bottom of the first quarter filtration chamber with I. sibirica exhibited the best average CODCr, NH4+-N and TN removal percentages in both the warm season (83.6%, 82.7% and 76.8%) and the cool season (66.3%, 44.1% and 43.8%). Therefore, this study indicated that the combination of aerating at the bottom of the first quarter filtration chamber and planting with I. sibirica in the HSSF CWs would be a promising way forward for wastewater treatment, especially in low temperature seasons.

Effects of design parameters, microbial community and nitrogen removal on the field-scale multi-pond constructed wetlands

Ecological multi-pond constructed wetlands (CWs) are an alternative wastewater treatment technology for nitrogen removal from non-point source pollution. As an important component of nitrogen cycles in the field-scale CWs, microorganisms are affected by design parameters. Nevertheless, the mechanism of design parameters affecting the distribution of microbial community and removal performance remains largely unexplored. In this study, satisfactory nitrogen removal performance was obtained in three multi-pond CWs. The highest mass removal rate per square meter (1104.0 mg/m²/day) and mass removal rate per cubic meter (590.2 mg/m³/day) for total nitrogen removal were obtained in the XY CW system during the wet season. The changes in seasonal parameters accounted for different removal performances and distributions of the microbial community. The combination of wastewater treatment technologies in the XY CW system consisting of ponds, CWs, and eco-floating treatment wetlands enriched the abundances of nitrogen-related functional genera. Correlation network analysis further demonstrated that longer hydraulic residence time and higher nitrogen concentration could intensify the enrichment of nitrogen-related functional genera. Regulating the combination of wastewater treatment technologies, the nitrogen concentration of influent, hydraulic loading rate, and water depth might promote the accumulation of microbial communities and enhance nitrogen removal. Macroscopical spatial/temporal regulation were proposed to enhance the treatment of non-point source pollution. The clarification of driving mechanism on design parameters, microbial community, and removal performance provided a novel perspective on the long-term maintenance of purification performance, practically sustainable applications, and scientific management of field-scale multi-pond CWs.

Influences of Dimethyl Phthalate on Bacterial Community and Enzyme Activity in Vertical Flow Constructed Wetland

Dimethyl phthalate (DMP), belonging to the family of Phthalate esters (PAEs), is a plasticizer and has been widely used in the world for many years. Nowadays, it has become a ubiquitous environmental pollutant and is listed as an environmental priority pollutant by China’s Environmental Monitoring Center. The purpose of this study is to estimate the responses of the bacterial community and enzyme activity to DMP contamination in three vertical flow constructed wetlands (VFCW), namely the constructed wetland A (planted with Pennisetum sinese Roxb), constructed wetland B (planted with Pennisetum purpureum Schum.), and constructed wetland C (unplanted), respectively. The results showed that the relative percentages of some genera associated with nitrogen metabolism and the function of degrading aromatic hydrocarbons were increased by DMP contamination, such as Dechloromonas agitata, Pleomorphomonas sp., Denitratisoma oestradiolicum, Plasticicumulans lactativorans, Novosphingobium sp., Alicycliphilus denitrificans, and Thauera sp. Meanwhile, principal coordinate analysis (PCA) analysis showed that the addition of DMP divided 12 samples into two groups as followed: one was the DMP group containing a-1, a-2, b-1, b-2, c-1 and c-2 while the other was no DMP group including A-1, A-2, B-1, B-2, C-1 and C-2. It indicated that DMP was the main reason for this change. In addition, by monitoring the activity of substrate enzymes, the activity of urease, phosphatase, catalase, and invertase in the wetlands before and after the experiment, these were significantly higher in the upper layer than in the lower layer and maintained high activity. Ultimately, the average influent concentration of DMP in three VFCWs was 8.12 mg/L and the average removal efficiency of the effluent was over 90%. Our results suggested that DMP was an important factor affecting the microbial community structure of wetland and the upper layer of the VFCW was the main site for the degradation of DMP. VFCW has great potential for the removal of the high concentration of DMP and it can be a good choice for the treatment of PAEs.

Investigation on the treatment effect of slope wetland on pollutants under different hydraulic retention times

This work was aimed at investigating the feasibility of the slope wetland system (SWs) for improving the polluted river water. According to the characteristics of polluted river water with different hydraulic retention time (HRT) changes, a field simulation device was set up. In this experiment, a SWs simulation device was set up to study pollutant removal of SWs under different hydraulic conditions. It was found that the effect of mixed fillers (zeolite and ceramsite) as the bed was better than that of the gravel fillers as the bed. The improvement of each treatment index was about 5% (P < 0.05). When HRT = 5 days, the removal rate of chemical oxygen demand (COD) was 28.02%, total nitrogen (TN) was 32.99%, ammonia nitrogen (NH₃-N) was 32.49%, and total phosphorus (TP) was 38.15%. At the same time, it was found that the characteristic moderate extension of HRT is conducive to the removal of pollutants in SWs. The growth of plants in the environment of the gravel matrix was worse than that of mixed fillers (zeolite and ceramsite). It was found that physical adsorption was the main form of pollution removal on the SWs fillers by Fourier infrared spectrum (FTIR) analysis. Based on the analysis of the microbial community in the packing of the device, it is indicated that the enrichment of microorganisms appeared during the experiment, forming the dominant bacteria against the polluted river water.

Effects of plant on denitrification pathways in integrated vertical-flow constructed wetland treating swine wastewater

Plant is an important part of constructed wetland (CW), while, its potential effect on nitrogen cycling is complicated. Herein, integrated vertical-flow constructed wetland (IVCW) in pilot-scale planted with Arundo donax (Planted System, PS) was constructed to treat swine wastewater. The removal performance of nitrogen in PS, effects of plant on the microbial community structure and nitrogen related function genes were revealed. Results showed that, Arundo donax planting enhanced the removal rate of TN, compared to unplanted IVCWs, the absolute abundance of Pseudomonas, Acinetobacter and Bacillus in PS was significantly increased, as well as the absolute abundance of functional gene (amoA, nxrA, nirK, nirS and nosZ). The denitrification process was mainly occurred in down-flow cell of PS with significantly higher abundant of nirK and nosZ (P < 0.05). These findings suggested that Arundo donax planting in IVCWs with zeolite as substrate promoted the growth of denitrifying microorganisms under higher pollutant load. In addition, the increased abundant of nosZ and the ratio of nosZ/∑nir indicating a lower genetic potential for N₂O release. Our research provides new insight into the potential application of plant on the purification of swine wastewater.

Community, Distribution, and Ecological Roles of Estuarine Archaea

Archaea are diverse and ubiquitous prokaryotes present in both extreme and moderate environments. Estuaries, serving as links between the land and ocean, harbor numerous microbes that are relatively highly active because of massive terrigenous input of nutrients. Archaea account for a considerable portion of the estuarine microbial community. They are diverse and play key roles in the estuarine biogeochemical cycles. Ammonia-oxidizing archaea (AOA) are an abundant aquatic archaeal group in estuaries, greatly contributing estuarine ammonia oxidation. Bathyarchaeota are abundant in sediments, and they may involve in sedimentary organic matter degradation, acetogenesis, and, potentially, methane metabolism, based on genomics. Other archaeal groups are also commonly detected in estuaries worldwide. They include Euryarchaeota, and members of the DPANN and Asgard archaea. Based on biodiversity surveys of the 16S rRNA gene and some functional genes, the distribution and abundance of estuarine archaea are driven by physicochemical factors, such as salinity and oxygen concentration. Currently, increasing amount of genomic information for estuarine archaea is becoming available because of the advances in sequencing technologies, especially for AOA and Bathyarchaeota, leading to a better understanding of their functions and environmental adaptations. Here, we summarized the current knowledge on the community composition and major archaeal groups in estuaries, focusing on AOA and Bathyarchaeota. We also highlighted the unique genomic features and potential adaptation strategies of estuarine archaea, pointing out major unknowns in the field and scope for future research.

Planktonic Bacterial and Archaeal Communities in an Artificially Irrigated Estuarine Wetland: Diversity, Distribution, and Responses to Environmental Parameters

Bacterial and archaeal communities play important roles in wetland ecosystems. Although the microbial communities in the soils and sediments of wetlands have been studied extensively, the comprehensive distributions of planktonic bacterial and archaeal communities and their responses to environmental variables in wetlands remain poorly understood. The present study investigated the spatiotemporal characteristics of the bacterial and archaeal communities in the water of an artificially irrigated estuarine wetland of the Liaohe River, China, explored whether the wetland effluent changed the bacterial and archaeal communities in the Liaohe River, and evaluated the driving environmental factors. Within the study, 16S rRNA quantitative PCR methods and MiSeq high-throughput sequencing were used. The bacterial and archaeal 16S rRNA gene abundances showed significant temporal variation. Meanwhile, the bacterial and archaeal structures showed temporal but not spatial variation in the wetland and did not change in the Liaohe River after wetland drainage. Moreover, the bacterial communities tended to have higher diversity in the wetland water in summer and in the scarce zone, while a relatively higher diversity of archaeal communities was found in autumn and in the intensive zone. DO, pH and PO₄-P were proven to be the essential environmental parameters shaping the planktonic bacterial and archaeal community structures in the Liaohe River estuarine wetland (LEW). The LEW had a high potential for methanogenesis, which could be reflected by the composition of the microbial communities.

Anaerobic ammonium-oxidizing bacteria in river water treatment wetland

Anaerobic ammonium-oxidizing (anammox) bacteria play an essential part in nitrogen removal in constructed wetlands. The objective of the present study was to explore the spatiotemporal dynamics of anammox bacterial communities and the associated factors in a full-scale constructed wetland for the treatment of polluted surface water. The abundance and diversity of anammox bacterial communities were characterized using quantitative polymerase chain reaction (PCR) and clone library analysis, respectively. Anammox bacterial diversity, richness, and abundance in the treatment wetland differed considerably among sampling sites and seasons, whereas anammox bacterial community structure tended to change slightly with site and time. Anammox abundance was likely influenced by temperature and the contents of nitrate and nitrite nitrogen. The increase of carbon and nitrogen contents could lower wetland anammox bacterial diversity and richness. Moreover, anammox bacterial diversity, richness, and abundance were also affected by wetland vegetation type. Candidatus Brocadia dominated in the treatment wetland, whereas Candidatus Kuenenia and a novel anammox phylotype were also detected. This work could provide some new insights towards anaerobic ammonium oxidization in surface water treatment wetland.

Impacting Microbial Communities and Absorbing Pollutants by Canna Indica and Cyperus Alternifolius in a Full-Scale Constructed Wetland System

Wetland plants that cover the wetlands play an important role in reducing pollutants. The aim of this study was to investigate the effect of two plant species on microbial communities and nitrogen-removal genes and to evaluate the contributions of absorbing pollutants by Canna indica (CI) and Cyperus alternifolius (CA) to the removal performance in both a vertical subsurface flow constructed wetland and a horizontal subsurface flow constructed wetland, which were part of a full-scale hybrid constructed wetland system. The microbial assemblages were determined using 16S rRNA high-throughput sequencing. Results showed that the presence of CI and CA positively affected microbial abundance and community in general and which was positive for the total bacteria and ammonia nitrogen removal in the CWs. The higher abundance of Nitrospirae appeared in the non-rhizosphere sediment (NRS) than that in the rhizosphere sediment (RS). More denitrification genes were found in NRS than in RS. The copy numbers of narG, nirS and nosZ genes for CA were higher than those for CI. Wetland plant species can significantly (P < 0.05) affect the distribution of microbial communities in RS. Plant selection is important to promote the development of microbial communities with a more active and diverse catabolic capability and the contribution of plant absorption to the overall removal rate of wetland system can be neglected.

The distribution of sediment bacterial community in mangroves across China was governed by geographic location and eutrophication

Bacterial community is an important component of mangrove ecosystem and can participate in the cycling of elements and promote plant growth. However, the biogeographic distribution pattern of mangrove bacterial community and the associated factors remain poorly known. The present study explored the biogeographic distribution of sediment bacterial community in six mangroves across China. At each mangrove, sediments were collected from both Avicennia marina-planted zones and intertidal mudflats. The community abundance, richness, diversity and structure of sediment bacteria differed greatly among mangrove wetlands. Plantation showed a positive influence on sediment bacterial abundance, richness and diversity. Proteobacteria was the largest bacterial phylum in sediments. The biogeographic distribution of bacterial community in mangroves across China was driven by the variables associated with the wetland trophic status as well as other physicochemical factors (e.g., salinity).

Changes in bacterial diversity and catabolic gene abundance during the removal of dimethylphenol isomers in laboratory-scale constructed wetlands

Constructed wetlands (CWs) are well-established wastewater treatment technologies and applied for bioremediation of contaminated water. Despite the optimal performance of CWs, the understanding of the bacterial processes in the rhizosphere, where mainly microbial degradation processes take place, is still limited. In the present study, laboratory-scale CWs planted with Juncus effusus and running under controlled conditions were studied in order to evaluate removal efficiency of dimethylphenols (DMPs), also in comparison to an unplanted bed. Next to removal rates, the bacterial community structure, diversity, and distribution, their correlation with physiochemical parameters, and abundance of the phenol hydroxylase gene were determined. As a result, better removal performance of DMP isomers (3,4-, 3,5-, and 2,6-DMP added as singles compounds or in mixtures) and ammonium loads, together with a higher diversity index, bacterial number, and phenol hydroxylase gene abundance in Juncus effusus CW in comparison with the non-planted CW, indicates a clear rhizosphere effect in the experimental CWs. An enhancement in the DMP removal and the recovery of the phenol hydroxylase gene were found during the fed with the DMP mixture. In addition, the shift of bacterial community in CWs was found to be DMP isomer dependent. Positive correlations were found between the bacteria harboring the phenol hydroxylase gene and communities present with 3,4-DMP and 3,5-DMP isomers, but not with the community developed with 2,6-DMP. These results indicate that CWs are highly dynamic ecosystems with rapid changes in bacterial communities harboring functional catabolic genes.

Variation of Bacterial and Archaeal Community Structures in a Full-Scale Constructed Wetlands for Wastewater Treatment

Microorganisms play important roles in the reduction of organic and inorganic pollutants in constructed wetlands used for the treatment of wastewater. However, the diversity and structure of microbial community in constructed wetland system remain poorly known. In this study, the Illumina MiSeq Sequencing of 16S rDNA was used to analyze the bacterial and archaeal microbial community structures of soil and water in a free surface flow constructed wetland, and the differences of bacterial communities and archaeal compositions between soil and water were compared. The results showed that the Proteobacteria were the dominant bacteria, making up 35.38%~48.66% relative abundance. Euryarchaeotic were the absolute dominant archaea in the influent sample with the relative abundance of 93.29%, while Thaumarchaeota showed dominance in the other three samples, making up 50.58%~75.70%. The relative abundances of different species showed great changes in bacteria and archaea, and the number of dominant species in bacteria was much higher than that in archaea. Compared to archaea, the community compositions of bacteria were more abundant and the changes were more significant. Meanwhile, bacteria and archaea had large differences in compositions between water and soil. The microbial richness in water was significantly higher than that in soil. Simultaneously, soil had a significant enrichment effect on some microbial flora.

Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages

BACKGROUND

As a recently discovered member of the DPANN superphylum, Woesearchaeota account for a wide diversity of 16S rRNA gene sequences, but their ecology, evolution, and metabolism remain largely unknown.

RESULTS

Here, we assembled 133 global clone libraries/studies and 19 publicly available genomes to profile these patterns for Woesearchaeota. Phylogenetic analysis shows a high diversity with 26 proposed subgroups for this recently discovered archaeal phylum, which are widely distributed in different biotopes but primarily in inland anoxic environments. Ecological patterns analysis and ancestor state reconstruction for specific subgroups reveal that oxic status of the environments is the key factor driving the distribution and evolutionary diversity of Woesearchaeota. A selective distribution to different biotopes and an adaptive colonization from anoxic to oxic environments can be proposed and supported by evidence of the presence of ferredoxin-dependent pathways in the genomes only from anoxic biotopes but not from oxic biotopes. Metabolic reconstructions support an anaerobic heterotrophic lifestyle with conspicuous metabolic deficiencies, suggesting the requirement for metabolic complementarity with other microbes. Both lineage abundance distribution and co-occurrence network analyses across diverse biotopes confirmed metabolic complementation and revealed a potential syntrophic relationship between Woesearchaeota and methanogens, which is supported by metabolic modeling. If correct, Woesearchaeota may impact methanogenesis in inland ecosystems.

CONCLUSIONS

The findings provide an ecological and evolutionary framework for Woesearchaeota at a global scale and indicate their potential ecological roles, especially in methanogenesis.

Inoculation with bacteria in floating treatment wetlands positively modulates the phytoremediation of oil field wastewater

The aim of the present study was to investigate the potential of plant-bacterial synergism in floating treatment wetlands (FTWs) for efficient remediation of an oil field wastewater. Two plants, Brachiara mutica and Phragmites australis, were vegetated on floatable mats to develop FTWs, and inoculated with bacterial cons which were then inoculated with a consortium of hydrocarbon-degrading bacteria (Bacillus subtilis strain LORI66, Klebsiella sp. strain LCRI87, Acinetobacter Junii strain TYRH47, Acinetobacter sp. strain LCRH81). Both plants successfully removed organic and inorganic pollutants from wastewater, but bioaugmentation of P. australis significantly enhanced the plant's efficiency to reduce oil content (97%), COD (93%), and BOD (97%), in wastewater. Analysis of alkane-degrading gene (alkB) abundance and its expression profile further validated a higher microbial growth and degradation activity in water around P. australis as well as its roots and shoots. This study provides insight into the available phytotechnology for remediation of crude oil-contaminated water and introduces a wetland macrophyte, P. australis, with tailor-made bacterial consortium as an effective tool for improved phytoremediation efficiency of FTWs.

Spatio-temporal shifts in the archaeal community of a constructed wetland treating river water

The distribution of archaeal community and the associated environmental variables in constructed wetland (CW), especially in free water surface flow CW (FWSF-CW), remain poorly understood. The present study explored the spatial and temporal dynamics of archaeal community in an FWSF-CW used for surface water treatment and evaluated the driving environmental variables. The archaeal density varied considerably among sites and seasons, ranging from 3.37×10⁸ to 3.59×10⁹ 16S rRNA gene copies per gram dry sediment/soil. The archaeal population density was adversely affected by high temperatures and tended to be lower during summer than during spring and winter. Moreover, considerable spatio-temporal variations of archaeal richness, diversity and community structure also occurred in the FWSF-CW. Higher nutrient contents correlated with a lower archaeal richness and diversity. Nitrate and carbon/nitrogen ratio were found to play important roles in shaping the overall archaeal community structure. Euryarchaeota and Bathyarchaeota were the dominant archaeal phyla in wetland sediments, while Thaumarchaeota tended to be dominant in wetland soils. In addition, the wetland archaeal community was related to vegetation type.

Vertical distribution of microbial communities in soils contaminated by chromium and perfluoroalkyl substances

Both Bacteria and Archaea are important players in soil biogeochemical cycles. Both chromium (Cr) and perfluoroalkyl substances (PFASs) are widely present in soil environment. However, the depth-related distribution of microbial community in soils contaminated by Cr or/and PFASs remains unknown. Hence, the present study applied quantitative PCR assay and Illumina MiSeq sequencing to investigate the vertical variations of archaeal and bacterial communities in soils (0.5-12.5m depth) contaminated by chrome plating waste and the potential effects of Cr and PFASs. Both bacterial and archaeal communities displayed the remarkable depth-related changes of abundance (2.16×10⁷-5.05×10⁹ and 4.95×10⁵-2.56×10⁸ 16S rRNA gene copies per gram dry soil respectively for Bacteria and Archaea), diversity (bacterial and archaeal Shannon diversity indices of 5.06-6.34 and 2.91-4.61, respectively) and structure. However, at each soil depth, bacterial community had higher abundance, richness and diversity than archaeal community. Soil bacterial communities were mainly composed of Proteobacteria, Chloroflexi, Actinobacteria and Firmicutes, and archaeal communities were dominated by Thaumarchaeota and unclassified Archaea. Moreover, microbial abundance and richness increased with increasing perfluorohexane sulfonate (PFHxS) content. Microbial abundance was correlated to total Cr, and archaeal richness was correlated to total Cr and Cr(IV). In addition, total Cr might be a key determinant of soil microbial community structure.

First Insights into the Diverse Human Archaeome: Specific Detection of Archaea in the Gastrointestinal Tract, Lung, and Nose and on Skin

Human-associated archaea remain understudied in the field of microbiome research, although in particular methanogenic archaea were found to be regular commensals of the human gut, where they represent keystone species in metabolic processes. Knowledge on the abundance and diversity of human-associated archaea is extremely limited, and little is known about their function(s), their overall role in human health, or their association with parts of the human body other than the gastrointestinal tract and oral cavity. Currently, methodological issues impede the full assessment of the human archaeome, as bacteria-targeting protocols are unsuitable for characterization of the full spectrum of Archaea. The goal of this study was to establish conservative protocols based on specifically archaea-targeting, PCR-based methods to retrieve first insights into the archaeomes of the human gastrointestinal tract, lung, nose, and skin. Detection of Archaea was highly dependent on primer selection and the sequence processing pipeline used. Our results enabled us to retrieve a novel picture of the human archaeome, as we found for the first time Methanobacterium and Woesearchaeota (DPANN superphylum) to be associated with the human gastrointestinal tract and the human lung, respectively. Similar to bacteria, human-associated archaeal communities were found to group biogeographically, forming (i) the thaumarchaeal skin landscape, (ii) the (methano)euryarchaeal gastrointestinal tract, (iii) a mixed skin-gastrointestinal tract landscape for the nose, and (iv) a woesearchaeal lung landscape. On the basis of the protocols we used, we were able to detect unexpectedly high diversity of archaea associated with different body parts.

In summary, our study highlights the importance of the primers and NGS data processing pipeline used to study the human archaeome. We were able to establish protocols that revealed the presence of previously undetected Archaea in all of the tissue samples investigated and to detect biogeographic patterns of the human archaeome in the gastrointestinal tract, on the skin, and for the first time in the respiratory tract, i.e., the nose and lungs. Our results are a solid basis for further investigation of the human archaeome and, in the long term, discovery of the potential role of archaea in human health and disease.

Aerobic and anaerobic methanotrophic communities in urban landscape wetland

Both aerobic methane-oxidizing bacteria (MOB) and nitrite-dependent anaerobic methane oxidation (n-damo) organisms can be important methane sinks in a wetland. However, the influences of the vegetation type on aerobic MOB and n-damo communities in wetland, especially in constructed wetland, remain poorly understood. The present study investigated the influences of the vegetation type on both aerobic MOB and n-damo organisms in a constructed urban landscape wetland. Sediments were collected from eight sites vegetated with different plant species. The abundance (1.19-3.27 × 10⁷ pmoA gene copies per gram dry sediment), richness (Chao1 estimator = 16.3-81.5), diversity (Shannon index = 2.10-3.15), and structure of the sediment aerobic MOB community were found to vary considerably with sampling site. In contrast, n-damo community abundance (8.74 × 10⁵-4.80 × 10⁶ NC10 16S rRNA gene copies per gram dry sediment) changed slightly with the sampling site. The richness (Chao1 estimator = 1-11), diversity (Shannon index = 0-0.78), and structure of the NC10 16S rRNA gene-based n-damo community illustrated slight site-related changes, while the spatial changes of the pmoA gene-based n-damo community richness (Chao1 estimator = 1-8), diversity (Shannon index = 0-0.99), and structure were considerable. The vegetation type could have a profound impact on the wetland aerobic MOB community and had a stronger influence on the pmoA-based n-damo community than on the NC10 16S-based one in urban wetland. Moreover, the aerobic MOB community had greater abundance and higher richness and diversity than the n-damo community. Methylocystis (type II MOB) predominated in urban wetland, while no known type I MOB species was detected. In addition, the ratio of total organic carbon to total nitrogen (C/N) might be a determinant of sediment n-damo community diversity and aerobic MOB richness.

The effects of climate, catchment land use and local factors on the abundance and community structure of sediment ammonia-oxidizing microorganisms in Yangtze lakes

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play important roles in regulating the nitrification process in lake ecosystems. However, the relative effects of climate, catchment land use and local conditions on the sediment ammonia-oxidizing communities in lakes remain unclear. In this study, the diversity and abundance of AOA and AOB communities were investigated in ten Yangtze lakes by polymerase chain reaction (PCR), clone library and quantitative PCR techniques. The results showed that the abundances of both AOA and AOB in bare sediments were considerably but not significantly higher than those in vegetated sediments. Interestingly, AOB communities were more sensitive to changes in local environmental factors and vegetation characteristics than were AOA communities. Amongst climate and land use variables, mean annual precipitation, percentage of agriculture and percentage of vegetation were the key determinants of AOB abundance and diversity. Additionally, total organic carbon and chlorophyll-a concentrations in lake water were significantly related to AOB abundance and diversity. The results of the ordination analysis indicated that 81.2 and 84.3% of the cumulative variance for the species composition of AOA and AOB communities could be explained by the climate, land use and local factors. The climate and local environments played important roles in shaping AOA communities, whereas catchment agriculture and water chlorophyll-a concentration were key influencing factors of AOB communities. Our findings suggest that the composition and structure of sediment ammonia-oxidizing communities in Yangtze lakes are strongly influenced by different spatial scale factors.

Unraveling Core Functional Microbiota in Traditional Solid-State Fermentation by High-Throughput Amplicons and Metatranscriptomics Sequencing

Fermentation microbiota is specific microorganisms that generate different types of metabolites in many productions. In traditional solid-state fermentation, the structural composition and functional capacity of the core microbiota determine the quality and quantity of products. As a typical example of food fermentation, Chinese Maotai-flavor liquor production involves a complex of various microorganisms and a wide variety of metabolites. However, the microbial succession and functional shift of the core microbiota in this traditional food fermentation remain unclear. Here, high-throughput amplicons (16S rRNA gene amplicon sequencing and internal transcribed space amplicon sequencing) and metatranscriptomics sequencing technologies were combined to reveal the structure and function of the core microbiota in Chinese soy sauce aroma type liquor production. In addition, ultra-performance liquid chromatography and headspace-solid phase microextraction-gas chromatography-mass spectrometry were employed to provide qualitative and quantitative analysis of the major flavor metabolites. A total of 10 fungal and 11 bacterial genera were identified as the core microbiota. In addition, metatranscriptomic analysis revealed pyruvate metabolism in yeasts (genera Pichia, Schizosaccharomyces, Saccharomyces, and Zygosaccharomyces) and lactic acid bacteria (genus Lactobacillus) classified into two stages in the production of flavor components. Stage I involved high-level alcohol (ethanol) production, with the genus Schizosaccharomyces serving as the core functional microorganism. Stage II involved high-level acid (lactic acid and acetic acid) production, with the genus Lactobacillus serving as the core functional microorganism. The functional shift from the genus Schizosaccharomyces to the genus Lactobacillus drives flavor component conversion from alcohol (ethanol) to acid (lactic acid and acetic acid) in Chinese Maotai-flavor liquor production. Our findings provide insight into the effects of the core functional microbiota in soy sauce aroma type liquor production and the characteristics of the fermentation microbiota under different environmental conditions.