Distribution Of Archaeal Communities Research Articles

Responses of applied voltages on the archaea microbial distribution in sludge digestion

As the development of urban population led to the increase of domestic water consumption, consequently the generation of surplus sludge (SS) produced increasingly during sewage treatment processes. In order to enhance the SS resource utilization efficiency, an electricity-assisted anaerobic digestion (EAAD) system was employed to examine the alterations in the digestion broth and the characteristics of gas production. Additionally, the response of applied voltages on the distribution of archaeal community near various electrodes within the sludge was explored. The results revealed that the application of high voltages exceeding 3.0 V hindered the CH4 production but stimulated the CO2 generation. Subsequently, both CH4 and CO2 production were impeded by the applied voltages. Furthermore, the increased voltages significantly decreased the abundance of Methanomicrobia, Methanosaeta, and Methanosarcina, which were crucial determinants of CH4 content in biogas. Notably, the excessively high voltages intensities caused the AD process to halt and even inactivate the microbial flora. Interestingly, the distribution characteristics of archaeal community were influenced not only by the voltages intensity but also exhibited variations between the anode and cathode regions. Moreover, as the applied voltage intensified, the discrepancy of responses between the cathode and anode regions became more pronounced, offering novel theoretical and technical foundations for the advancement of electricity-assisted with AD technology.

Bacterial and Archaeal Community Distribution in Oilfield Water Re-injection Facilities and the Influences from Microorganisms in Injected Water.

Water flooding is widely employed for oil production worldwide. However, there has never been a systematic investigation of the microbial communities occurring in oilfield water re-injection facilities. Here, we investigated the distribution of bacterial and archaeal communities in water re-injection facilities of an oilfield, and illustrated the combined influences of environmental variation and the microorganisms in injected water on the microbial communities. Bacterial communities from the surface injection facilities were dominated by aerobic or facultative anaerobic Betaproteobacteria, Alphaproteobacteria, and Flavobacteria, whereas Clostridia, Deltaproteobacteria, Anaerolineae, and Synergistia predominated in downhole of the injection wells, and Gammaproteobacteria, Betaproteobacteria, and Epsilonproteobacteria predominated in the production wells. Methanosaeta, Methanobacterium, and Methanolinea were dominant archaea in the injection facilities, while Methanosaeta, Methanomethylovorans, and Methanoculleus predominated in the production wells. This study also demonstrated that the microorganisms in injected water could be easily transferred from injection station to wellheads and downhole of injection wells, and environmental variation and diffusion-limited microbial transfer resulted from formation filtration were the main factors determining microbial community assembly in oil-bearing strata. The results provide novel information on the bacterial and archaeal communities and the underlying mechanisms occurring in oilfield water re-injection facilities, and benefit the development of effective microbiologically enhanced oil recovery and microbiologically prevented reservoir souring programs.

Identifying Microbial Distribution Drivers of Archaeal Community in Sediments from a Black-Odorous Urban River—A Case Study of the Zhang River Basin

Rapid urbanization has destroyed urban water systems and led to blackened and odorous rivers. The heavily polluted rivers are always facing eutrophication and heavy metal pollution, while the combined effects of these environmental factors on the microbial diversity and distribution of the river microbial communities have not been adequately reported, especially the archaeal communities. In this study, we investigated the community structure and microbial distribution of sediment archaeal communities from an urban blackened and odorous river basin of the Zhang river, in Nanling, China. Results showed that the archaeal community from the eight sediment sites have average values of Shannon and Chao1 at 3.4921 and 232.7202, respectively. The community diversity and richness were different among samples. Halobacterota and Euryarchaeota were the most abundant phylum and Crenarchaeota also took up a considerable amount of the archaeal community. To reveal the main environmental drivers of the distribution of archaeal communities in sediment, the environmental physicochemical factors (total nitrogen, total phosphorus, oxidation/reduction potential, nitrate nitrogen, ammonia nitrogen, pH and total organic carbon) and heavy metals (Cr, Ni, Cu, Zn, As, Cd, Pb and Hg) in sediment were determined. A redundancy analysis (RDA) revealed that Eh was the most prominent influencing factor, and As was the most influential heavy metal on the microbial distribution of archaeal communities. Furthermore, a variance partitioning analysis (VPA) was used to identify the impacts of physicochemical factors and heavy metals on the archaeal community distribution. Results showed that heavy metals have higher effects on archaeal community distribution than physicochemical factors. The present study suggested that the heavy metal pollution should be paid more attention in the microbial distribution in heavily polluted urban rivers, and also should be taken into consideration for improving the efficacies of ecological evaluation and remediation.

Distribution of archaeal community in the mud pit during strong-flavor baijiu fermentation

Multi-species solid-state fermentation in a mud pit is one of the typical features of strong-flavor baijiu, in which archaea plays important roles, however, the archaeal community distribution and diversity during fermentation are still lack of research. The biomass, composition and succession of archaea communities in fermented grains and pit mud were analyzed by high throughput sequencing. The potential interaction between archaea and bacteria was analyzed by co-occurrence network. Results demonstrate that the average biomass of archaea in pit mud was about 200 times higher than that of fermented grains. There was no significant difference in archaeal community structure between fermented grains and pit mud (r=0.017, P=0.074), but succession patterns between them showed significant correlation (r=0.30, P=0.03). Methanobacterium was the most abundant archaea in fermented grains and pit mud, and other dominant groups included Methanosarcina, Methanocorpusculum, Methanoculleus, and Methanobrevibacter. The co-occurrence network analysis showed that Methanobacterium was positively correlated with most bacteria in fermented grains and pit mud, especially with Hydrogenispora and Caproiciproducens, the dominant bacteria in pit mud. Our results revealed the temporal and spatial distribution characteristics and potential functions of the archaeal community in the mud pit of strong-flavor baijiu.

Termite Societies Promote the Taxonomic and Functional Diversity of Archaeal Communities in Mound Soils.

Recent studies involving microbial communities in termite mounds have been more focused on bacteria and fungi with little attention given to archaea, which play significant roles in nutrient cycling. Thus, we aimed at characterizing the archaeal taxonomic and functional diversity in two termite mound soils using the shotgun sequencing method with the assumption that termite activities could promote archaeal diversity. Our findings showed that termite mound soils have archaeal groups that are taxonomically different from their surrounding soils, with Euryarchaeota, Korarchaeota, and Nanoarchaeota being predominant while Thaumarchaeota and Crenarchaeota were predominant in the surrounding soils. Additionally, the observed nutrient pathways: phosphorus, nitrogen, and sulfur were all significantly more predominant in termite mound soils than in their comparative surrounding soils. Alpha diversity showed that archaea were not significantly different within termite mound soils and the surrounding soils. The beta diversity revealed significant differences in the archaeal taxonomic composition and their functional categories between the termite mounds and surrounding soils. Our canonical correspondence analysis revealed that the distribution of archaeal communities was likely dependent on the soil properties. Our results suggested that termite activities may promote the diversity of archaea; with some of our sequences grouped as unclassified archaea, there is a need for further research to unveil their identity.

Different Diversity and Distribution of Archaeal Community in the Aqueous and Oil Phases of Production Fluid From High-Temperature Petroleum Reservoirs.

To get a better knowledge on how archaeal communities differ between the oil and aqueous phases and whether environmental factors promote substantial differences on microbial distributions among production wells, we analyzed archaeal communities in oil and aqueous phases from four high-temperature petroleum reservoirs (55–65°C) by using 16S rRNA gene based 454 pyrosequencing. Obvious dissimilarity of the archaeal composition between aqueous and oil phases in each independent production wells was observed, especially in production wells with higher water cut, and diversity in the oil phase was much higher than that in the corresponding aqueous phase. Statistical analysis further showed that archaeal communities in oil phases from different petroleum reservoirs tended to be more similar, but those in aqueous phases were the opposite. In the high-temperature ecosystems, temperature as an environmental factor could have significantly affected archaeal distribution, and archaeal diversity raised with the increase of temperature (p < 0.05). Our results suggest that to get a comprehensive understanding of petroleum reservoirs microbial information both in aqueous and oil phases should be taken into consideration. The microscopic habitats of oil phase, technically the dispersed minuscule water droplets in the oil could be a better habitat that containing the indigenous microorganisms.

Distribution of Archaeal Communities along the Coast of the Gulf of Finland and Their Response to Oil Contamination.

The Baltic Sea is vulnerable to environmental changes. With the increasing shipping activities, the risk of oil spills remains high. Archaea are widely distributed in many environments. However, the distribution and the response of archaeal communities to oil contamination have rarely been investigated in brackish habitats. Hence, we conducted a survey to investigate the distribution, diversity, composition, and species interactions of indigenous archaeal communities at oil-contaminated sites along the coast of the Gulf of Finland (GoF) using high-throughput sequencing. Surface water and littoral sediment samples were collected at presumably oil-contaminated (oil distribution facilities) and clean sites along the coastline of the GoF in the winter 2015 and the summer 2016. Another three samples of open sea surface water were taken as offshore references. Of Archaea, Euryarchaeota dominated in the surface water and the littoral sediment of the coast of the GoF, followed by Crenarchaeota (including Thaumarchaeota, Thermoprotei, and Korarchaeota based on the Greengenes database used). The unclassified sequences accounted for 5.62% of the total archaeal sequences. Our study revealed a strong dependence of the archaeal community composition on environmental variables (e.g., salinity, pH, oil concentration, TOM, electrical conductivity, and total DNA concentration) in both littoral sediment and coastal water in the GoF. The composition of archaeal communities was season and ecosystem dependent. Archaea was highly diverse in the three ecosystems (littoral sediment, coastal water, and open sea water). Littoral sediment harbored the highest diversity of archaea. Oil was often detected in the littoral sediment but rarely detected in water at those presumably contaminated sites. Although the composition of archaeal community in the littoral sediment was sensitive to low-input oil contamination, the unchanged putative functional profiles and increased interconnectivity of the archaeal core species network plausibly revealed resilience and the potential for oil degradation. Halobacteriaceae and putative cytochrome P450 pathways were significantly enriched in the oil-contaminated littoral sediment. The archaeal taxa formed highly interconnected and interactive networks, in which Halobacteriaceae, Thermococcus, and methanogens were the main components, implying a potential relevant trophic connection between hydrocarbon degradation, methanogenesis, sulfate reduction, and/or fermentative growth.

Bacterial and archaeal community distribution and stabilization of anaerobic sludge in a strengthen circulation anaerobic (SCA) reactor for municipal wastewater treatment

In this study, a SCA reactor was employed for municipal wastewater treatment at a mesophilic temperature (30°C) under different hydraulic retention times (HRT) and upflow velocities (Vup) to investigate granule sludge stability and spatial microbial distribution. The stable COD removal efficiency readied at HRT of 15, 12, 9 and 6h, and Vup ranging from 0.6 to 5.9mh−1. EPS fraction analysis of granule sludge shows that municipal wastewater was mainly attributed to the enrichment influence of polysaccharide and tightly bound-EPS. SEM images exhibited that the stability and floating of anaerobic granular sludge may be promoted in the primary three-phase separator area because the channels of the granules was clogged by EPS. The SMA and high-throughput sequencing analysis indicated acetoclastic methanogens and hydrogenotrophic methanogens played an important role in formation and maintenance of the anaerobic granule sludge in low and high organic load rate operation conditions.

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.

Spatial Distribution and Molecular Diversity of Archaeal Communities in the Extreme Hypersaline Meromictic Brâncoveanu Lake (Transylvanian Basin, Romania)

ABSTRACTDating from the Middle Miocene, the massive halite deposits lying beneath the Transylvanian Basin (Central Romania) have been valuable mineral resources quarried for millennia. Among the numerous hypersaline pit lakes that resulted from this mining, Brâncoveanu Lake is unique by its extreme salinity. Assessment of physicochemical variables, water chemistry and trophic status indicated that Brâncoveanu Lake is a permanently stratified, pH-neutral, NaCl-rich and eutrophied system. We investigated the abundance, molecular diversity and vertical distribution of archaeal community by culture-independent approaches. Additionally, the most relevant environmental parameters shaping the archaeal community composition were evaluated by statistical methods. Archaea appeared to largely outnumber Bacteria; altogether the great prevalence of Halobacteriaceae-related sequences could imply a major contribution of this group to the biogeochemical carbon turnover. The fairly distinct composition of archaeal communities reflects the lake's physicochemical stratification. Among the limnological factors, salinity and oxygen showed a significant impact on determining the composition and structure of archaeal assemblages. Furthermore, Brâncoveanu Lake might harbor novel microorganisms such as members of the recently described phylum Nanohaloarchaea. Overall, this study reported the occurrence of halophilic Archaea in a little explored hydrogeochemical system and provided a better insight into geomicrobiology of meromictic hypersaline pit lakes.

Investigation of Archaeal and Bacterial community structure of five different small drinking water networks with special regard to the nitrifying microorganisms

Total microbial community structure, and particularly nitrifying communities inhabiting five different small drinking water networks characterized with different water physical and chemical parameters was investigated, using cultivation-based methods and sequence aided Terminal Restriction Fragment Length Polymorphism (T-RFLP) analysis. Ammonium ion, originated from well water, was only partially oxidized via nitrite to nitrate in the drinking water distribution systems. Nitrification occurred at low ammonium ion concentration (27–46μM), relatively high pH (7.6–8.2) and over a wide range of dissolved oxygen concentrations (0.4–9.0mgL−1). The nitrifying communities of the distribution systems were characterized by variable most probable numbers (2×102–7.1×104 MPN L−1) and probably originated from the non-treated well water. The sequence aided T-RFLP method revealed that ammonia-oxidizing microorganisms and nitrite-oxidizing Bacteria (Nitrosomonas oligotropha, Nitrosopumilus maritimus, and Nitrospira moscoviensis, ‘Candidatus Nitrospira defluvii’) were present in different ratios in the total microbial communities of the distinct parts of the water network systems. The nitrate generated by nitrification was partly utilized by nitrate-reducing (and denitrifying) Bacteria, present in low MPN and characterized by sequence aided T-RFLP as Comamonas sp. and Pseudomonas spp. Different environmental factors, like pH, chemical oxygen demand, calculated total inorganic nitrogen content (moreover nitrite and nitrate concentration), temperature had important effect on the total bacterial and archaeal community distribution.

The putative functional ecology and distribution of archaeal communities in sponges, sediment and seawater in a coral reef environment.

Archaea play crucial roles in a number of key ecological processes including nitrification and methanogenesis. Although several studies have been conducted on these organisms, the roles and dynamics of coral reef archaeal communities are still poorly understood, particularly in host and nonhost biotopes and in high (HMA) and low microbial abundance (LMA) sponges. Here, archaeal communities detected in six distinct biotopes, namely, sediment, seawater and four different sponge species Stylissa carteri, Stylissa massa, Xestospongia testudinaria and Hyrtios erectus from the Spermonde Archipelago, SW Sulawesi, Indonesia were investigated using 454-pyrosequencing of 16S rRNA genes (OTU cut-off 97%). Archaeal communities from sediment and sponges were dominated by Crenarchaeota, while the seawater community was dominated by Euryarchaeota. The biotope explained almost 75% of the variation in archaeal composition, with clear separation between microbial assemblages from sediment, X.testudinaria and H.erectus (HMA). In contrast, samples from seawater and both Stylissa species (LMA) showed considerable overlap in the ordination and, furthermore, shared most abundant OTUs with the exception of a single dominant OTU specifically enriched in both Stylissa species. Predicted functional gene content in archaeal assemblages also revealed significant differences among biotopes. Different ammonia assimilation strategies were exhibited by the archaeal communities: X.testudinaria, H.erectus and sediment archaeal communities were enriched for glutamate dehydrogenase with mixed specificity (NAD(P)(+) ) pathways, while archaeal planktonic communities were enriched for specific glutamate dehydrogenase (NADP(+) ) and glutamate synthase pathways. Archaeal communities in Stylissa had intermediate levels of enrichment. Our results indicate that archaeal communities in different biotopes have distinct ecophysiological roles.

Archaeal and anaerobic methane oxidizer communities in the Sonora Margin cold seeps, Guaymas Basin (Gulf of California)

Cold seeps, located along the Sonora Margin transform fault in the Guaymas Basin, were extensively explored during the 'BIG' cruise in June 2010. They present a seafloor mosaic pattern consisting of different faunal assemblages and microbial mats. To investigate this mostly unknown cold and hydrocarbon-rich environment, geochemical and microbiological surveys of the sediments underlying two microbial mats and a surrounding macrofaunal habitat were analyzed in detail. The geochemical measurements suggest biogenic methane production and local advective sulfate-rich fluxes in the sediments. The distributions of archaeal communities, particularly those involved in the methane cycle, were investigated at different depths (surface to 18 cm below the sea floor (cmbsf)) using complementary molecular approaches, such as Automated method of Ribosomal Intergenic Spacer Analysis (ARISA), 16S rRNA libraries, fluorescence in situ hybridization and quantitative polymerase chain reaction with new specific primer sets targeting methanogenic and anaerobic methanotrophic lineages. Molecular results indicate that metabolically active archaeal communities were dominated by known clades of anaerobic methane oxidizers (archaeal anaerobic methanotroph (ANME)-1, -2 and -3), including a novel 'ANME-2c Sonora' lineage. ANME-2c were found to be dominant, metabolically active and physically associated with syntrophic Bacteria in sulfate-rich shallow sediment layers. In contrast, ANME-1 were more prevalent in the deepest sediment samples and presented a versatile behavior in terms of syntrophic association, depending on the sulfate concentration. ANME-3 were concentrated in small aggregates without bacterial partners in a restricted sediment horizon below the first centimetres. These niche specificities and syntrophic behaviors, depending on biological surface assemblages and environmental availability of electron donors, acceptors and carbon substrates, suggest that ANME could support alternative metabolic pathways than syntrophic anaerobic oxidation of methane.

Temporal distribution of the archaeal community in the Changjiang Estuary hypoxia area and the adjacent East China Sea as determined by denaturing gradient gel electrophoresis and multivariate analysis

The archaeal community and the effects of environmental factors on microbial community distribution were investigated at five sampling sites in the Changjiang Estuary hypoxia area and the adjacent East China Sea in June, August, and October 2006. Profiles of the archaeal communities were generated by denaturing gradient gel electrophoresis of 16S rRNA genes followed by DNA sequence analysis, and the results were analyzed by multivariate statistical analysis. Denaturing gradient gel electrophoresis band patterns were analyzed by cluster analysis to assess temporal changes in the genetic diversity of the archaeal communities. Most of the October samples grouped together separately from those of June and August. Analysis of DNA sequences revealed that the dominant archaeal groups in the Changjiang Estuary hypoxia area and the adjacent East China Sea were affiliated with Euryarchaeota (mainly marine group II) and Crenarchaeota. The effects of environmental factors on the archaeal community distribution were analyzed by the ordination technique of canonical correspondence analysis. Salinity had a significant effect on the archaeal community composition.