Assessment of active methanogenic archaea in a methanol-fed upflow anaerobic sludge blanket reactor

Methanogenic archaea enrichment of a granular sludge was undertaken in an upflow anaerobic sludge blanket (UASB) reactor fed with methanol in order to enrich methylotrophic and hydrogenotrophic methanogenic populations. A microbial community assessment, in terms of microbial composition and activity—throughout the different stages of the feeding process with methanol and acetate—was performed using specific methanogenic activity (SMA) assays, quantitative real-time polymerase chain reaction (qPCR), and high-throughput sequencing of 16S ribosomal RNA (rRNA) genes from DNA and complementary DNA (cDNA). Distinct methanogenic enrichment was revealed by qPCR of mcrA gene in the methanol-fed community, being two orders of magnitude higher with respect to the initial inoculum, achieving a final mcrA/16S rRNA ratio of 0.25. High-throughput sequencing analysis revealed that the resulting methanogenic population was mainly composed by methylotrophic archaea (Methanomethylovorans and Methanolobus genus), being also highly active according to the RNA-based assessment. SMA confirmed that the methylotrophic pathway, with a direct conversion of methanol to CH₄, was the main step of methanol degradation in the UASB. The biomass from the UASB, enriched in methanogenic archaea, may bear great potential as additional inoculum for bioreactors to carry out biogas production and other related processes.     

Does allelopathy affect co-culturing <Emphasis Type="Italic">Haslea ostrearia</Emphasis> with other microalgae relevant to aquaculture?

Haslea ostrearia is a marine diatom known to produce marennine, a water-soluble blue-green pigment responsible for the greening of oysters in ponds along the French Atlantic coast. This phenomenon occurs seasonally when H. ostrearia blooms in oyster ponds, and it increases the economic value of cultured oysters. From an ecological perspective, H. ostrearia blooms are accompanied by a decrease in the abundance of other microalgae, suggesting that this diatom produces allelochemicals. Recent studies showed that purified marennine has other biological activities, for instance antioxidant, antibacterial, and antiviral activities, which could be used in aquaculture to promote this pigment as a natural antipathogen agent. One important issue regarding the possible use of H. ostrearia in aquaculture as a mixed algal diet, however, is the importance of marennine allelopathy. In this study, we investigated the allelopathic effect of H. ostrearia on the growth of five microalgal species relevant to aquaculture: Chaetoceros calcitrans, Skeletonema costatum, Phaeodactylum tricornutum, Tetraselmis suecica, and Tisochrysis lutea. Allelopathic tests were realized by co-culturing these microalgae with H. ostrearia in batch and in semi-continuous mode, based on initial biovolume ratios. Our findings showed that inhibition of the growth of microalgae due to the presence of H. ostrearia and marennine was species dependent. Skeletonema costatum, C. calcitrans, and T. lutea were significantly more sensitive, whereas T. suecica and P. tricornutum appeared to be more resistant. Growth irradiance significantly influenced the allelopathic effect against the sensitive species S. costatum, and the H. ostrearia production of marennine increases with irradiance. Data presented in this study partly support the hypothesis that marennine released into the culture medium possibly acts as an allelochemical compound, thus explaining the dominance of H. ostrearia and the loss of sensitive algae in oyster ponds, but also that some species are insensitive, which allows co-culturing and use in a mixed algal diet in aquaculture.     

Temporal and spatial impact of <Emphasis Type="Italic">Spartina alterniflora</Emphasis> invasion on methanogens community in Chongming Island,China

Methane production by methanogens in wetland is recognized as a significant contributor to global warming. Spartina alterniflora (S. alterniflora), which is an invasion plant in China’s wetland, was reported to have enormous effects on methane production. But studies on shifts in the methanogen community in response to S. alterniflora invasion at temporal and spatial scales in the initial invasion years are rare. Sediments derived from the invasive species S. alterniflora and the native species Phragmites australis (P. australis) in pairwise sites and an invasion chronosequence patch (4 years) were analyzed to investigate the abundance and community structure of methanogens using quantitative real-time PCR (qPCR) and Denaturing gradient gel electrophoresis (DGGE) cloning of the methyl-coenzyme M reductase A (mcrA) gene. For the pairwise sites, the abundance of methanogens in S. alterniflora soils was lower than that of P. australis soils. For the chronosequence patch, the abundance and diversity of methanogens was highest in the soil subjected to two years invasion, in which we detected some rare groups including Methanocellales and Methanococcales. These results indicated a priming effect at the initial invasion stages of S. alterniflora for microorganisms in the soil, which was also supported by the diverse root exudates. The shifts of methanogen communities after S. alterniflora invasion were due to changes in pH, salinity and sulfate. The results indicate that root exudates from S. alterniflora have a priming effect on methanogens in the initial years after invasion, and the predominate methylotrophic groups (Methanosarcinales) may adapt to the availability of diverse substrates and reflects the potential for high methane production after invasion by S. alterniflora.     

Distribution and ecological relations among the alien crab, <Emphasis Type="Italic">Percnon gibbesi</Emphasis> (H. Milne-Edwards 1853) and autochthonous species,in and out of an SW Mediterranean MPA

The distribution of the allochthonous crab Percnon gibbesi and its relationships with other benthic invertebrate species was assessed inside the marine reserve of Cabo de Palos—Islas Hormigas (Mediterranean sea, Spain) and neighbouring non-protected sites. Although a significant spatial variability was detected at finer spatial scale, there was no influence of protection measures or insularity on the abundance of P. gibbesi. The presence of small holes, encrusting algae and low slope favour the colonization success of this crustacean, and the spatial distribution of these habitat features could explain the observed pattern. The abundance of P. gibbesi was similar to that of native crab species; however, a non-significant negative relationship between the abundance of P. gibbesi and native crabs (Pachygrapsus marmoratus and Eriphia verrucosa), urchins (Arbacia lixula and Paracentrotus lividus) and a snail (Phorcus turbinatus) was observed. This work highlights the importance of monitoring alien crab population densities taking structural habitat and other potentially influential factors into account and the likely effect of this alien species on the native ones.     

Native ecosystem engineer facilitates recruitment of invasive crab and native invertebrates

Native ecosystem engineers that add physical structure to ecosystems can facilitate invasive species. In this study we determined the effects of the native tube-forming serpulid worm, Galeolaria caespitose on the recruitment of the invasive New Zealand porcelain crab, Petrolisthes elongatus, and whether invasive crab recruitment was related to the recruitment of native species. P. elongatus is abundant beneath intertidal rocks around Tasmania, southern Australia, and the underside of these rocks is usually covered with a calcareous matrix formed by the serpulid. We used an experimental approach to investigate whether rocks, serpulids on the underside of rocks and adult P. elongatus influenced the recruitment P. elongatus and native communities. P. elongatus and native invertebrates only recruited in the presence of rocks indicating the importance of rock as primary recruitment habitat. Moreover, the presence of serpulids on the underside of rocks significantly increased the recruitment of P. elongatus and native invertebrates compared to rocks without serpulids. Rocks with higher densities of adult P. elongatus at the end of the experiment also had higher densities of P. elongatus recruits. The density of P. elongatus recruits did not influence native species richness and abundance although there was some evidence that high P. elongatus recruitment was correlated with shifts in native community structure. We have shown that a native ecosystem engineer facilitates recruitment of an invasive crab but this does not appear to influence the recruitment of native species.     

Seasonal dynamics of ammonia-oxidizing microorganisms in freshwater aquaculture ponds

An annual investigation into the abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in fresh water aquaculture ponds was performed by quantitative PCR of the amoA gene. The results showed that AOB were the main ammonia-oxidizing microorganisms in water, and significantly higher copy numbers of the AOB amoA gene were observed in the summer (Aug 2012), while no significant differences were detected among the other three seasons. AOA showed low abundances throughout the year. The predominance of AOB in aquaculture water was suggested to be related to photoinhibition. Both the AOB and AOA amoA genes in aquaculture pond sediments showed typical seasonal patterns. The maximum density of AOB was observed in the autumn (Nov 2012) and winter (Jan 2013), while the maximum density of AOA was observed in winter. The minimum densities of both AOA and AOB occurred in the summer. The concentration of the AOA amoA gene was higher than that of the AOB amoA gene in sediments by almost one order of magnitude, which indicates that AOA are the dominant ammonia-oxidizing microorganisms in the aquaculture pond sediments. Dissolved oxygen is suggested to be the key factor determining the predominance of AOA in pond sediments.     

Study of biological communities subject to imperfect detection: bias and precision of community <Emphasis Type="Italic">N</Emphasis>-mixture abundance models in small-sample situations

Community N-mixture abundance models for replicated counts provide a powerful and novel framework for drawing inferences related to species abundance within communities subject to imperfect detection. To assess the performance of these models, and to compare them to related community occupancy models in situations with marginal information, we used simulation to examine the effects of mean abundance \((\bar{\lambda }\): 0.1, 0.5, 1, 5), detection probability \((\bar{p}\): 0.1, 0.2, 0.5), and number of sampling sites (n _site : 10, 20, 40) and visits (n _visit : 2, 3, 4) on the bias and precision of species-level parameters (mean abundance and covariate effect) and a community-level parameter (species richness). Bias and imprecision of estimates decreased when any of the four variables \((\bar{\lambda }\), \(\bar{p}\), n _site , n _visit ) increased. Detection probability \(\bar{p}\) was most important for the estimates of mean abundance, while \(\bar{\lambda }\) was most influential for covariate effect and species richness estimates. For all parameters, increasing n _site was more beneficial than increasing n _visit . Minimal conditions for obtaining adequate performance of community abundance models were n _site  ≥ 20, \(\bar{p}\) ≥ 0.2, and \(\bar{\lambda }\) ≥ 0.5. At lower abundance, the performance of community abundance and community occupancy models as species richness estimators were comparable. We then used additive partitioning analysis to reveal that raw species counts can overestimate β diversity both of species richness and the Shannon index, while community abundance models yielded better estimates. Community N-mixture abundance models thus have great potential for use with community ecology or conservation applications provided that replicated counts are available.     

Dietary Supplement of Medicinal Herbal Leaf Powder on Growth Performance,Digestive Enzymes Activities,Energy Utilization and Vitamin Levels of the Freshwater Prawn <Emphasis Type="Italic">Macrobrachium rosenbergii</Emphasis>

Experiments were conducted to evaluate the influence of dietary supplement (@ 5%) dried leaf powder of the medicinal herbs, Ocimum sanctum, Solanum trilobatum and Phyllanthus amarus on survival, growth, activities of digestive enzymes, energy utilization, and vitamin contents of the freshwater prawn, Macrobrachium rosenbergii. Results indicated significant (P < 0.05) improvements in survival, growth, activities of digestive enzymes, energy utilization, and vitamin levels in herb supplemented feeds fed prawns group compared to prawns fed non-herbs feed. Best growth was noted in prawns fed with the feed supplemented by leaf powder of P. amarus, followed by S. trilobatum and O. sanctum. It is concluded that leaf powder of these herbs can be used as dietary supplement for better growth of freshwater prawn.     

Surface–sediment diatom assemblages of the urban ponds of St. Petersburg,Russia

The diatom assemblages of the surface sediments have been studied in 53 urban ponds and lakes of St. Petersburg for the first time. In total, 350 species and infraspecific taxa have been registered; the species of Achnanthidium, Cocconeis, Cyclostephanos, Cyclotella, Gomphonema, Lemnicola, Navicula, Nitzschia, and Stephanodiscus genera were the most common. The wide distribution of small centric planktonic taxa, Cyclostephanos dubius, C. invisitatus, Cyclotella pseudostelligera, Stephanodiscus hantzschii, and S. minutulus, is preconditioned by the depletion of dissolved silica, which is a result of the high phosphorus load. The high abundance of macrophytes in the shallowest sites favors the dominance of epiphytic Fragilaria, Staurosira, and Staurosirella taxa. Bottom-living diatoms in the shallow eutrophic and hypereutrophic urban ponds are light-limited; this is a result of either macrophytes or phytoplankton development. Alkaliphilous and alkalibiontic species prevail among the pH-indicative species, while eutraphentic and hypereutraphentic diatoms, as well as those thriving in a wide range of trophic conditions, dominate over other trophic groups. The β- and α-mesosaprobic species are the most common saprobity-indicative taxa.     

Comparison of bioethanol production from cultivated versus wild <Emphasis Type="Italic">Gracilaria verrucosa</Emphasis> and <Emphasis Type="Italic">Gracilaria gigas</Emphasis>

The seaweed genus Gracilaria is a potential candidate for the production of bioethanol due to its high carbohydrate content. Gracilaria is abundant throughout the world and can be found in both wild and cultivated forms. Differences in the ecological factors such as temperature, salinity, and light intensity affecting wild and cultivated specimens may influence the biochemical content of seaweeds, including the carbohydrate content. This study aimed to investigate the proximate composition and potential bioethanol production of wild and cultivated G. gigas and G. verrucosa. Bioethanol was produced using separate hydrolysis fermentation (SHF), employing a combination of enzymatic and acid hydrolysis, followed by fermentation with Saccharomyces cerevisiae ATCC 200062. The highest carbohydrate content was found in wild G. gigas. The highest galactose and glucose contents (20.21 ± 0.32 and 9.70 ± 0.49 g L^?1, respectively), as well as the highest production of bioethanol (3.56 ± 0.02 g L^?1), were also found in wild G. gigas. Thus, we conclude that wild G. gigas is the most promising candidate for bioethanol production. Further research is needed to optimize bioethanol production from wild G. gigas. Domestication of wild G. gigas is a promising challenge for aquaculture to avoid overexploitation of this wild seaweed resource.     

The invasive mud crab enforces a major shift in a rocky littoral invertebrate community of the Baltic Sea

In rocky littoral communities, intense herbivory allows for the occurrence of trophic cascades where higher trophic levels influence producer communities. Invasive predators can be especially effective in imposing trophic cascades. The North American mud crab Rhithropanopeus harrisii is a recent invader in the Baltic Sea, with an expanding distribution range. Here, we document the effects of mud crab on the native invertebrate community associated with the key foundation species Fucus vesiculosus. During the initial 3 years of invasion, mud crab abundance in F. vesiculosus increased from 2 % to about 25 % of the algae being inhabited by crabs. Simultaneously, the invertebrate community underwent a major transition: Species richness and diversity dropped as a consequence of decreasing abundance and the loss of certain taxa. The abundance of gastropods decreased by 99 % and that of crustaceans by 75 %, while chironomids completely disappeared. Consequently, the community dominated earlier by herbivorous and periphyton-grazing gastropods and crustaceans shifted to a mussel dominated community with overall low abundances of herbivores. At the same time filamentous epiphytic algae prospered and the growth rate of F. vesiculosus decreased. We suggest that this shift in the invertebrate community may have far reaching consequences on ecosystem functioning. These arise through changes in the strength of producer–herbivore interaction, caused by mud crab predation on the dominating grazer taxa. This interaction is a major determinant of ecological function of ecosystems, i.e. productivity and energy flow to higher trophic levels. Therefore, the decrease in herbivory can be expected to have a major structuring role in producer communities of the rocky littoral macroalgal assemblages.     

Anaerobic cellulolytic microbial communities decomposing the biomass of <Emphasis Type="Italic">Anabaena variabilis</Emphasis>

Four previously isolated methanogenic anaerobic consortia, which were originally cultivated on a cellulose-containing substrate (filter paper), were used as inocula for the anaerobic conversion of the biomass of Anabaena variabilis into biogas at 55°C. The cumulative methane yield in the biogas produced by the most active consortia reached 64%. However, the biotransformation was only efficient in the course of the single inoculation and pretreatment of the cyanobacterial biomass by its concentration and freeze-thawing. The DGGE analysis of the structure of the selected microbial consortia, cultivated on the filter paper, revealed qualitative variations in the biodiversity of predominant Bacteria, showing differences in band number and intensity. The composition of methanogenic Archaea in these consortia was similar, with the presence of the genera Methanoculleus and Methanosarcina. The efficiency of the microbial consortia selection, and the role of the various microbial trophic groups in bioconversion of the substrates, such as cellulose and the biomass of phototrophic microorganisms are discussed.     

Conspecific tolerance and heterospecific competition as mechanisms for overcoming resistance to invasion by an intertidal crab

The success of the invasive Asian shore crab, Hemigrapsus sanguineus, stems partly from its ability to exclude established crab species from preferred rocky and cobble intertidal habitat. Here, we assessed preference and competition for habitat types (cobble vs. sand) for H. sanguineus and two competitor species; the previous invasive green crab, Carcinus maenas, and the native rock crab, Cancer irroratus, in New England. In simple laboratory experiments, we paired similarly sized heterospecifics and conspecifics from each species, and also grouped combinations of C. maenas and H. sanguineus in a series of four-individual sets in order to dissect the outcome of intra- and inter-specific competition at different densities. Individually, all three species preferred cobble substrate. With paired conspecifics, H. sanguineus individuals would cohabitate in cobble, whereas C. maenas and C. irroratus individuals each excluded conspecifics from cobble. In heterospecific pairs, H. sanguineus excluded both C. maenas and C. irroratus from cobble. C. maenas and C. irroratus, were equally likely to exclude the other species, but rarely excluded H. sanguineus. In larger assemblages, H. sanguineus preferentially grouped under cobble, whereas C. maenas were more evenly distributed among habitat types. These observations demonstrate that conspecific tolerance and heterospecific competition can be effective, complementary mechanisms for overcoming invasion resistance. Such mechanisms help explain the well-studied success of H. sanguineus following its introduction into New England coastal habitats, and the resulting exclusion of preexisting crab species.     

Diversity of methanogenic archaea from the 2012 terrestrial hot spring (Valley of Geysers,Kamchatka)

Archaeal diversity in the 2012 terrestrial hot spring (Valley of Geysers, Kronotsky Nature Reserve, Kamchatka, Russia) was investigated using molecular and cultivation-based approaches. Analysis of the 16S rRNA gene sequences revealed predominance among archaea of uncultured microorganisms of the pSL12 and THSCG clusters. Analysis of the mcrA genes revealed that members of the order Methanomassiliicoccales were predominant (68%) among methanogens; the latter constituted 0.15% of the total number of archaea. Five stable thermophilic methanogenic associations utilizing hydrogen, formate, acetate, or methanol as substrates were obtained from the sediments of spring 2012. The diversity of cultured methanogens was limited to members of the genera Methanothermobacter, Methanothrix, and Methanomethylovorans. The association growing at 65°C and producing methane from methanol contained two components, which probably formed a syntrophic relationship: a Methanothermobacter methanogenic archaeon and a bacterium representing an separate cluster within the Firmicutes phylum, which was phylogenetically related to the genera Thermacetogenium and Syntrophaceticus. These data indicate high diversity of methanogens, notwithstanding their low abundance among archaea. The group of thermophilic Methanomassiliicoccales, which predominated among methanogens, is of special interest.     

Deep sequencing analysis of bacterial community structure of Soldhar hot spring,India

We investigated the bacterial community structure of Soldhar hot spring with extreme high temperature 95°C located in Uttarakhand, India using high throughput sequencing. Bacterial phyla Proteobacteria (88.8%), Deinococcus-Thermus (7.5%), Actinobacteria (2.3%), and Firmicutes (1.07%) were predominated in the sequencing survey, whereas Bacteroidetes, Verrucomicrobia, Aquificae and Acidobacteria were detected in relatively lower abundance in Soldhar hot spring. At the family level, Comamonadaceae (52.5%), Alteromonadaceae (15.9%), and Thermaceae (7.5%) were mostly dominated in the ecosystem followed by Chromatiaceae, Microbacteriaceae, and Cyclobacteriaceae. Besides, members of Rhodobacteraceae, Moraxellaceae, Xanthomonadaceae, Aquificaceae, Enterobacteriaceae, Bacillaceae, Methylophilaceae, etc. were detected as a relatively lower abundance. In the present study we discuss the overall microbial community structure and their relevance to the ecology of the Soldhar hot spring environment.     

Comparative analysis of deep sequenced methanogenic communities: identification of microorganisms responsible for methane production

Background

Although interactions between microorganisms involved in biogas production are largely uncharted, it is commonly accepted that methanogenic Archaea are essential for the process. Methanogens thrive in various environments, but the most extensively studied communities come from biogas plants. In this study, we employed a metagenomic analysis of deeply sequenced methanogenic communities, which allowed for comparison of taxonomic and functional diversity as well as identification of microorganisms directly involved in various stages of methanogenesis pathways.

Results

A comprehensive metagenomic approach was used to compare seven environmental communities, originating from an agricultural biogas plant, cattle-associated samples, a lowland bog, sewage sludge from a wastewater treatment plant and sediments from an ancient gold mine. In addition to the native consortia, two laboratory communities cultivated on maize silage as the sole substrate were also analyzed. Results showed that all anaerobic communities harbored genes of all known methanogenesis pathways, but their abundance varied greatly between environments and that genes were encoded by different methanogens. Identification of microorganisms directly involved in different stages of methane production revealed that hydrogenotrophic methanogens, such as Methanoculleus, Methanobacterium, Methanobrevibacter, Methanocorpusculum or Methanoregula, predominated in most native communities, whereas acetoclastic Methanosaeta seemed to be the key methanogen in the wastewater treatment plant. Furthermore, in many environments, the methylotrophic pathway carried out by representatives of Methanomassiliicoccales, such as Candidatus Methanomethylophilus and Candidatus Methanoplasma, seemed to play an important role in methane production. In contrast, in stable laboratory reactors substrate versatile Methanosarcina predominated.

Conclusions

The metagenomic approach presented in this study allowed for deep exploration and comparison of nine environments in which methane production occurs. Different abundance of methanogenesis-related functions was observed and the functions were analyzed in the phylogenetic context in order to identify microbes directly involved in methane production. In addition, a comparison of two metagenomic analytical tools, MG-RAST and MetAnnotate, revealed that combination of both allows for a precise characterization of methanogenic communities.

     

Effects of solid-phase denitrification on the nitrate removal and bacterial community structure in recirculating aquaculture system

A solid-phase denitrification (SPD) reactor packed with poly (3-hydroxybutyrate-co-3-hydroxyvalerate) as a carbon source was incorporated into a recirculating aquaculture system (RAS) to remove accumulated nitrate. Bacterial community structures in different parts of the RAS, including biofilter unit, SPD reactor, and culture water, were analyzed using Illumina MiSeq sequencing technology. The data showed that nitrate levels decreased remarkably in the RAS connected with SPD reactor (RAS-DR). In contrast, nitrate levels increased continuously in the conventional RAS without SPD reactor (RAS-CK). Biofilter unit and culture water in RAS-DR developed lower species richness and higher bacterial community diversity than that in RAS-CK. The bacterial community structure of RAS was significantly affected by the SPD process and the changes included an increase in the proportion of Proteobacteria and Firmicutes and a decrease in Nitrospira abundance in RAS-DR. Firmicutes was the most abundant phylum (56.9 %) and mainly consisted of Clostridium sensu stricto (48.3 %) in SPD reactor.     

Contrasting patterns of the bacterial and archaeal communities in a high-elevation river in northwestern China

The patterns of macrobiota in lotic ecosystems have been extensively explored, however, the dynamics of microbiota remain poorly investigated, especially in the high-elevation region. To address this deficit, we collected eight samples to unveil the bacterial and archaeal community in the Kaidu river, located at the arid region of northwestern China (an average of 2,500 m a.s.l.). For the bacterial community, phylogenetically Betaproteobacteria prevailed, followed by Alphaproteobacteria and Actinobacteria; at the finer genus level, Limnohabitans and Variovorax were prominent. Along the river, the bacterial community showed a continuous succession. Specifically, their α- and β-diversity gradually increased, suggesting a distance-decay pattern. Additionally, there was an ecological transition between the dominant and the rare sub-community along the river: the relative abundance of the dominant members gradually decreased as the rare members increased. We report that temperature and spatial distance were significantly related to the variation of bacterial community. Variance partitioning analysis showed that the environmental factors contributed more to the bacterial community than did the spatial distance. In the case of the archaeal community, the methanogenic groups, mainly Methanosaeta and Methanosarcina, were prominent within the Kaidu river. Unlike the continuous change in the patterns of the bacterial community, the archaeal community showed a constant pattern along the river. Our results showed that the archaeal community was independent of the environmental and spatial factors. We propose that the inoculation of soil-derived archaea is responsible for the archaeal community in the Kaidu river. Together, our study demonstrated that the bacterial community in the high-elevation Kaidu river is a continuum, whereas the archaeal community is not.     

Vertical profiles of microbial communities in perfluoroalkyl substance-contaminated soils

Poly- and perfluoroalkyl compounds (PFASs) are ubiquitous in the environment, but their influences on microbial community remain poorly known. The present study investigated the depth-related changes of archaeal and bacterial communities in PFAS-contaminated soils. The abundance and structure of microbial community were characterized using quantitative PCR and high-throughput sequencing, respectively. Microbial abundance changed considerably with soil depth. The richness and diversity of both bacterial and archaeal communities increased with soil depth. At each depth, bacterial community was more abundant and had higher richness and diversity than archaeal community. The structure of either bacterial or archaeal community displayed distinct vertical variations. Moreover, a higher content of perfluorooctane sulfonate (PFOS) could have a negative impact on bacterial richness and diversity. The rise of soil organic carbon content could increase bacterial abundance but lower the richness and diversity of both bacterial and archaeal communities. In addition, Proteobacteria, Actinobacteria, Chloroflexi, Cyanobacteria, and Acidobacteria were the major bacterial groups, while Thaumarchaeota, Euryarchaeota, and unclassified Archaea dominated in soil archaeal communities. PFASs could influence soil microbial community.