Archaeal Community Composition Research Articles

Hydrogenotrophic methanogenesis is the dominant methanogenic pathway in neotropical tank bromeliad wetlands.

Several thousands of tank bromeliads per hectare of neotropical forest create a unique wetland ecosystem that emits substantial amounts of CH4 . Tank bromeliads growing in the forest canopy (functional type-II tank bromeliads) were found to emit more CH4 than tank bromeliads growing on the forest floor (functional type-I tank bromeliads) but the reasons for this difference and the underlying microbial CH4 -cycling processes have not been studied. Therefore, we characterized archaeal communities in bromeliad tanks of the two different functional types in a neotropical montane forest of southern Ecuador using terminal-restriction fragment length polymorphism (T-RFLP) and performed tank-slurry incubations to measure CH4 production potential, stable carbon isotope fractionation and pathway of CH4 formation. The archaeal community composition was dominated by methanogens and differed between bromeliad functional types. Hydrogenotrophic Methanomicrobiales were the dominant methanogens and hydrogenotrophic methanogenesis was the dominant methanogenic pathway among all bromeliads. The relative abundance of aceticlastic Methanosaetaceae and the relative contribution of aceticlastic methanogenesis increased in type-I tank bromeliads probably due to more oxic conditions in type-I than in type-II bromeliads leading to the previously observed lower in situ CH4 emissions from type-I tank bromeliads but to higher CH4 production potentials in type-I tank bromeliad slurries.

Biogeographic distribution of bacterial, archaeal and methanogenic communities and their associations with methanogenic capacity in Chinese wetlands

Natural wetlands and anthropogenic paddy fields are the dominant biogenic sources of atmospheric methane emission which have been speculated as the most probable sources for the increase of post-2006 atmospheric methane. Regional differences in CH4 emission is possibly due to microbial biogeographic distribution. Here we collected soils from 19 wetlands from different regions in China. The methane production capacity (MPC) was measured for each soil samples and varied from 1.11 to 841.94mg/kg dry soil. High throughput sequencing was employed to investigate the diversity and composition of bacterial, archaeal and methanogenic communities. Similar biogeographic patterns for bacterial, archaeal and methanogenic communities along the latitudinal gradient were observed, and the biogeographic assemblies of different microbial groups were driven by concurrent factors, including edaphic variables (total organic carbon, total phosphorus and pH) and climatic variables (annual frost days, mean annual temperature, direct solar radiation and mean annual precipitation). MPC was significantly correlated with TOC concentration, and in addition, various functional taxa were positively correlated with MPC (P<0.05), for example, Sphingomonas, Syntrophomonas, Methanospirillum and Methanoregula, indicating their potential contributions in the methanogenic process, and many of them were fermentative bacteria and methanogens. Network analysis showed that some syntrophs, sulfate-reducers and methanogens were tightly co-occurred in one module, suggesting their involvements in cross-linked functional processes. Our study implicated both temperature and substrate availability altered the biogeographic patterns of microbial community as well as methane production potential in Chinese wetlands.

Prokaryotic Community Composition in Arctic Kongsfjorden and Sub-Arctic Northern Bering Sea Sediments As Revealed by 454 Pyrosequencing.

Fjords and continental shelves represent distinct marine ecosystems in the pan-arctic region. Kongsfjorden is a glacial fjord that is located on the west coast of Svalbard, and is influenced by both Atlantic and Arctic water masses. The Bering Sea consists of a huge continental shelf in the northeast and a deep ocean basin in the southwest, and is influenced by Pacific water. Microbial community compositions of Arctic sediment samples BJ4 from outer basin and BJ36 from inner basin of Kongsfjorden and sub-Arctic samples NEC5 from shallow shelf and DBS1 from deep basin region of the northern Bering Sea were investigated using 454 pyrosequencing of archaeal and bacterial 16S rRNA genes. Most archaeal sequences in the sediments were related to Thaumarchaeota, though Euryarchaeota were more abundant in the Arctic glacier-influencing inner basin sediment BJ36. Thaumarchaeota Group C3 was the dominant archaeal population in all samples. Proteobacteria and Bacteroidetes dominated the sediment bacterial communities. Acidobacteria and Actinobacteria were also dominant in the northern Bering Sea samples. Alphaproteobacteria and Epsilonproteobacteria were the two main classes in Kongsfjorden sediment bacterial communities while Deltaproteobacteria and Gammaproteobacteria were dominant in the northern Bering Sea sediments. Differences in the presence and abundance of other dominant archaeal and bacterial populations were observed among sediment samples. In contrast to archaeal community differences that the Arctic BJ36 archaeal community was distinct from the sub-Arctic sediments and the Arctic outer basin sediment BJ4, cluster analysis based on bacterial OTU (operational taxonomic unit) distributions indicated that the Arctic and sub-Arctic bacterial communities segregated from one another. These results suggest that the sediment archaeal and bacterial community compositions can be driven by different environmental factors. Differences in the presence and abundance of particular archaeal species (e.g., Candidatus Nitrosopumilus and Methanococcoides) or bacterial species (e.g., Sulfurimonas, Sulfurovum, and Desulfobulbaceae) involved in biogeochemical cycles were also observed among sediment samples. At the same time, despite the community variation, some phylotypes (e.g., Marinicella) were dominant in all sediments. This study indicates diverse microbial communities inhabiting pan-arctic marine sediments, and highlights potential roles for Archaea and Bacteria in global biogeochemical cycles in these environments.

Distinctive Soil Archaeal Communities in Different Variants of Tropical Equatorial Forest.

Little is known of how soil archaeal community composition and diversity differ between local variants of tropical rainforests. We hypothesized that (1) as with plants, animals, fungi, and bacteria, the soil archaeal community would differ between different variants of tropical forest; (2) that spatially rarer forest variants would have a less diverse archaeal community than common ones; (3) that a history of forest disturbance would decrease archaeal alpha- and beta-diversity; and (4) that archaeal distributions within the forest would be governed more by deterministic than stochastic factors. We sampled soil across several different forest types within Brunei, Northwest Borneo. Soil DNA was extracted, and the 16S rRNA gene of archaea was sequenced using Illumina MiSeq. We found that (1) as hypothesized, there are distinct archaeal communities for each forest type, and community composition significantly correlates with soil parameters including pH, organic matter, and available phosphorous. (2) As hypothesized, the "rare" white sand forest variants kerangas and inland heath had lower archaeal diversity. A nestedness analysis showed that archaeal community in inland heath and kerangas was mainly a less diverse subset of that in dipterocarp forests. However, primary dipterocarp forest had the lowest beta-diversity among the other tropical forest types. (3) Also, as predicted, forest disturbance resulted in lower archaeal alpha-diversity-but increased beta-diversity in contrast with our predictions. (4) Contrary to our predictions, the BetaNTI of the various primary forest types indicated community assembly was mainly stochastic. The possible effects of these habitat and disturbance-related effects on N cycling should be investigated.

Basin Scale Variation on the Composition and Diversity of Archaea in the Pacific Ocean.

The Archaea are a widely distributed group of prokaryotes that inhabit and thrive in many different environments. In the sea, they play key roles in various global biogeochemical processes. Here, in order to investigate the vertical profiles of archaeal community across a large geographic distance, the compositions of archaeal communities in seven seawater columns in the Pacific Ocean were investigated using high throughput 454 pyrosequencing of the 16S rRNA gene. The surface archaeal communities showed lower diversity and greater variability than those in the deeper layers. Two of the major archaeal phyla that displayed different depth preferences were Thaumarchaeota and Euryarchaeota. The majority of Thaumarchaeota belonged to Marine Group I (MGI), which had high relative abundance in deep water. In contrast, Euryarchaeota, which mainly consisted of Marine Group II (MGII) and III (MGIII), were dominant in the surface layer. Compared with MGI and MGII, MGIII were less abundant in seawater and generally absent from the surface water of the subarctic Pacific. In addition, niche separation in the MGI, MGII, and MGIII subgroups was also observed. For example, MGI.C and MGII.A (the major subgroups of MGI and MGII, respectively) displayed a strong negative correlation with each other. The highest level of archaeal diversity was found in the core of an oxygen minimum zone (OMZ) located off Costa Rica, which resulted from the co-occurrence of both anaerobic and aerobic archaea. For example, methanotrophic archaea ANME-2, methanogenic archaea and several sediment origin archaea, such as Marine Benthic Group A (MBGA) and Bathyarchaeota, were all detected at relatively high abundance in the OMZ. Together, our findings indicate that vertical heterogeneities along water columns and latitudinal differentiation in the surface waters are ubiquitous features of archaeal communities in the Pacific Ocean, and the OMZ off Costa Rica is an archaeal biodiversity hot-spot.

Transcription of mcrA Gene Decreases Upon Prolonged Non-flooding Period in a Methanogenic Archaeal Community of a Paddy-Upland Rotational Field Soil.

Methanogenic archaea survive under aerated soil conditions in paddy fields, and their community is stable under these conditions. Changes in the abundance and composition of an active community of methanogenic archaea were assessed by analyzing mcrA gene (encoding α subunit of methyl-coenzyme M reductase) and transcripts during a prolonged drained period in a paddy-upland rotational field. Paddy rice (Oryza sativa L.) was planted in the flooded field and rotated with soybean (Glycine max [L.] Merr.) under upland soil conditions. Soil samples were collected from the rotational plot in the first year, with paddy rice, and in the two successive years, with soybean, at six time points, before seeding, during cultivation, and after harvest as well as from a consecutive paddy (control) plot. By the time that soybean was grown in the second year, the methanogenic archaeal community in the rotational plot maintained high mcrA transcript levels, comparable with those of the control plot community, but the levels drastically decreased by over three orders of magnitude after 2years of upland conversion. The composition of active methanogenic archaeal communities that survived upland conversion in the rotational plot was similar to that of the active community in the control plot. These results revealed that mcrA gene transcription of methanogenic archaeal community in the rotational field was affected by a prolonged non-flooding period, longer than 1year, indicating that unknown mechanisms maintain the stability of methanogenic archaeal community in paddy fields last up to 1year after the onset of drainage.

Linseed Oil Supplementation of Lambs' Diet in Early Life Leads to Persistent Changes in Rumen Microbiome Structure.

Diet has been shown to have a significant impact on microbial community composition in the rumen and could potentially be used to manipulate rumen microbiome structure to achieve specific outcomes. There is some evidence that a window may exist in early life, while the microbiome is being established, where manipulation through diet could lead to long-lasting results. The aim of this study was to test the hypothesis that dietary supplementation in early life will have an effect on rumen microbial composition that will persist even once supplementation is ceased. Twenty-seven new-born lambs were allocated to one of three dietary treatments; a control group receiving standard lamb meal, a group receiving lamb meal supplemented with 40 g kg-1 DM of linseed oil and a group receiving the supplement pre-weaning and standard lamb meal post-weaning. The supplement had no effect on average daily feed intake or average daily weight gain of lambs. Bacterial and archaeal community composition was significantly (p = 0.033 and 0.005, respectively) different in lambs fed linseed oil throughout the study compared to lambs on the control diet. Succinivibrionaceae, succinate producers, and Veillonellaceae, propionate producers, were in a higher relative abundance in the lambs fed linseed oil while Ruminococcaceae, a family linked with high CH4 emitters, were in a higher relative abundance in the control group. The relative abundance of Methanobrevibacter was reduced in the lambs receiving linseed compared to those that didn’t. In contrast, the relative abundance of Methanosphaera was significantly higher in the animals receiving the supplement compared to animals receiving no supplement (40.82 and 26.67%, respectively). Furthermore, lambs fed linseed oil only in the pre-weaning period had a bacterial community composition significantly (p = 0.015) different to that of the control group, though archaeal diversity and community structure did not differ. Again, Succinivibrionaceae and Veillonellaceae were in a higher relative abundance in the group fed linseed oil pre-weaning while Ruminococcaceae were in a higher relative abundance in the control group. This study shows that lambs fed the dietary supplement short-term had a rumen microbiome that remained altered even after supplementation had ceased.

Long-term Fertilization Structures Bacterial and Archaeal Communities along Soil Depth Gradient in a Paddy Soil

Soil microbes provide important ecosystem services. Though the effects of changes in nutrient availability due to fertilization on the soil microbial communities in the topsoil (tilled layer, 0–20 cm) have been extensively explored, the effects on communities and their associations with soil nutrients in the subsoil (below 20 cm) which is rarely impacted by tillage are still unclear. 16S rRNA gene amplicon sequencing was used to investigate bacterial and archaeal communities in a Pup-Calric-Entisol soil treated for 32 years with chemical fertilizer (CF) and CF combined with farmyard manure (CFM), and to reveal links between soil properties and specific bacterial and archaeal taxa in both the top- and subsoil. The results showed that both CF and CFM treatments increased soil organic carbon (SOC), soil moisture (MO) and total nitrogen (TN) while decreased the nitrate_N content through the profile. Fertilizer applications also increased Olsen phosphorus (OP) content in most soil layers. Microbial communities in the topsoil were significantly different from those in subsoil. Compared to the CF treatment, taxa such as Nitrososphaera, Nitrospira, and several members of Acidobacteria in topsoil and Subdivision 3 genera incertae sedis, Leptolinea, and Bellilinea in subsoil were substantially more abundant in CFM. A co-occurrence based network analysis demonstrated that SOC and OP were the most important soil parameters that positively correlated with specific bacterial and archaeal taxa in topsoil and subsoil, respectively. Hydrogenophaga was identified as the keystone genus in the topsoil, while genera Phenylobacterium and Steroidobacter were identified as the keystone taxa in subsoil. The taxa identified above are involved in the decomposition of complex organic compounds and soil carbon, nitrogen, and phosphorus transformations. This study revealed that the spatial variability of soil properties due to long-term fertilization strongly shapes the bacterial and archaeal community composition and their interactions at both high and low taxonomic levels across the whole soil profile.

Effect of Pre-weaning Diet on the Ruminal Archaeal, Bacterial, and Fungal Communities of Dairy Calves.

At birth, calves display an underdeveloped rumen that eventually matures into a fully functional rumen as a result of solid food intake and microbial activity. However, little is known regarding the gradual impact of pre-weaning diet on the establishment of the rumen microbiota. Here, we employed next-generation sequencing to investigate the effects of the inclusion of starter concentrate (M: milk-fed vs. MC: milk plus starter concentrate fed) on archaeal, bacterial and anaerobic fungal communities in the rumens of 45 crossbred dairy calves across pre-weaning development (7, 28, 49, and 63 days). Our results show that archaeal, bacterial, and fungal taxa commonly found in the mature rumen were already established in the rumens of calves at 7 days old, regardless of diet. This confirms that microbiota colonization occurs in the absence of solid substrate. However, diet did significantly impact some microbial taxa. In the bacterial community, feeding starter concentrate promoted greater diversity of bacterial taxa known to degrade readily fermentable carbohydrates in the rumen (e.g., Megasphaera, Sharpea, and Succinivribrio). Shifts in the ruminal bacterial community also correlated to changes in fermentation patterns that favored the colonization of Methanosphaera sp. A4 in the rumen of MC calves. In contrast, M calves displayed a bacterial community dominated by taxa able to utilize milk nutrients (e.g., Lactobacillus, Bacteroides, and Parabacteroides). In both diet groups, the dominance of these milk-associated taxa decreased with age, suggesting that diet and age simultaneously drive changes in the structure and abundance of bacterial communities in the developing rumen. Changes in the composition and abundance of archaeal communities were attributed exclusively to diet, with more highly abundant Methanosphaera and less abundant Methanobrevibacter in MC calves. Finally, the fungal community was dominated by members of the genus SK3 and Caecomyces. Relative anaerobic fungal abundances did not change significantly in response to diet or age, likely due to high inter-animal variation and the low fiber content of starter concentrate. This study provides new insights into the colonization of archaea, bacteria, and anaerobic fungi communities in pre-ruminant calves that may be useful in designing strategies to promote colonization of target communities to improve functional development.

Thermoplasmatales and Methanogens: Potential Association with the Crenarchaeol Production in Chinese Soils.

Crenarchaeol is a unique isoprenoid glycerol dibiphytanyl glycerol tetraether (iGDGT) lipid, which is only identified in cultures of ammonia-oxidizing Thaumarchaeota. However, the taxonomic origins of crenarchaeol have been debated recently. The archaeal populations, other than Thaumarchaeota, may have associations with the production of crenarchaeol in ecosystems characterized by non-thaumarchaeotal microorganisms. To this end, we investigated 47 surface soils from upland and wetland soils and rice fields and another three surface sediments from river banks. The goal was to examine the archaeal community compositions in comparison with patterns of iGDGTs in four fractional forms (intact polar-, core-, monoglycosidic- and diglycosidic-lipid fractions) along gradients of environments. The DistLM analysis identified that Group I.1b Thaumarchaeota were mainly responsible for changes in crenarchaeol in the overall soil samples; however, Thermoplasmatales may also contribute to it. This is further supported by the comparison of crenarchaeol between samples characterized by methanogens, Thermoplasmatales or Group I.1b Thaumarchaeota, which suggests that the former two may contribute to the crenarchaeol pool. Last, when samples containing enhanced abundance of Thermoplasmatales and methanogens were considered, crenarchaeol was observed to correlate positively with Thermoplasmatales and archaeol, respectively. Collectively, our data suggest that the crenarchaeol production is mainly derived from Thaumarchaeota and partly associated with uncultured representatives of Thermoplasmatales and archaeol-producing methanogens in soil environments that may be in favor of their growth. Our finding supports the notion that Thaumarchaeota may not be the sole source of crenarchaeol in the natural environment, which may have implication for the evolution of lipid synthesis among different types of archaea.

Effects of biochar on CH4 emission with straw application on paddy soil

Straw incorporation, a common agricultural practice for improving soil quality in paddy soil, leads to the increase of methane (CH4) emission. Application of biochar in soil is an attractive method to sequestrate carbon and reduce the emission of greenhouse gas. This study aimed at exploring the effect of biochar on CH4 emission in the paddy soil with straw incorporation. In this study, the low-temperature biochar (BC300) and high-temperature biochar (BC500 and BC700) were incubated with or without straw in soil. Soil CH4 fluxes were monitored during the whole period of laboratory incubation. Soil properties were measured, including pH, redox potential (Eh) and dissolved organic carbon (DOC). The abundance and composition of methanogenic archaeal and methanotrophic bacterial communities were analyzed by real-time quantitative PCR (qPCR) and high-throughput sequencing, respectively. When no straw was applied, low-temperature biochar decreased soil Eh, increased the abundances of methanogenic archaea, and thus promoted the emission of CH4, while high-temperature biochar had little effect on CH4 emission. When straw was applied, biochar inhibited CH4 emission by decreasing the content of available carbon for methanogenic archaea. The inhibition effect of high-temperature biochar was stronger than that of low-temperature biochar. The results indicated that CH4 emission was affected by both biochar type and straw application. Biochar could significantly decrease CH4 emission when straw was returned to paddy soil, and the decrease induced by high-temperature biochar was stronger than that of low-temperature biochar.

Establishment of thermophilic anaerobic terephthalic acid degradation system through one-step temperature increase startup strategy – Revealed by Illumina Miseq Sequencing

Over recent years, thermophilic digestion was constantly focused owing to its various advantage over mesophilic digestion. Notably, the startup approach of thermophilic digester needs to be seriously considered as unsuitable startup ways may result in system inefficiency. In this study, one-step temperature increase startup strategy from 37 °C to 55 °C was applied to establish a thermophilic anaerobic system treating terephthalic acid (TA) contained wastewater, meanwhile, the archaeal and bacterial community compositions at steady periods of 37 °C and 55 °C during the experimental process was also compared using Illumina Miseq Sequencing. The process operation demonstrated that the thermophilic TA degradation system was successfully established at 55 °C with over 95% COD reduction. For archaea community, the elevation of operational temperature from 37 °C to 55 °C accordingly increase the enrichment of hydrogenotrophic methanogens but decrease the abundance of the acetotrophic ones. While for bacterial community, the taxonomic analysis suggested that Syntrophorhabdus (27.40%) was the dominant genus promoting the efficient TA degradation under mesophilic condition, whereas OPB95 (24.99%) and TA06 (14.01%) related populations were largely observed and probably take some crucial role in TA degradation under thermophilic condition.

Effect of urea-supplemented diets on the ruminal bacterial and archaeal community composition of finishing bulls.

In this study, we evaluated the effects of urea-supplemented diets on the ruminal bacterial and archaeal communities of finishing bulls using sequencing technology. Eighteen bulls were fed a total mixed ration based on maize silage and concentrate (40:60) and randomly allocated to one of three experimental diets: a basal diet with no urea (UC, 0%), a basal diet supplemented with low urea levels (UL, 0.8% dry matter (DM) basis), and a basal diet supplemented with high urea levels (UH, 2% DM basis). All treatments were iso-nitrogenous (14% crude protein, DM basis) and iso-metabolic energetic (ME=11.3MJ/kg, DM basis). After a 12-week feeding trial, DNA was isolated from ruminal samples and used for 16S rRNA gene amplicon sequencing. For bacteria, the most abundant phyla were Firmicutes (44.47%) and Bacteroidetes (41.83%), and the dominant genera were Prevotella (13.17%), Succiniclasticum (4.24%), Butyrivibrio (2.36%), and Ruminococcus (1.93%). Urea supplementation had no effect on most phyla (P>0.05), while there was a decreasing tendency in phylum TM7 with increasing urea levels (P=0.0914). Compared to UC, UH had lower abundance of genera Butyrivibrio and Coprococcus (P=0.0092 and P=0.0222, respectively). For archaea, the most abundant phylum was Euryarchaeota (99.81% of the sequence reads), and the most abundant genus was Methanobrevibacter (90.87% of the sequence reads). UH increased the abundance of genus Methanobrevibacter and Methanobacterium (P=0.0299 and P=0.0007, respectively) and decreased the abundance of vadinCA11 (P=0.0151). These findings suggest that urea-supplemented diets were associated with a shift in archaeal biodiversity and changes in the bacterial community in the rumen.

Differential responses of soil bacteria, fungi, archaea and protists to plant species richness and plant functional group identity.

Plants are known to influence belowground microbial community structure along their roots, but the impacts of plant species richness and plant functional group (FG) identity on microbial communities in the bulk soil are still not well understood. Here, we used 454-pyrosequencing to analyse the soil microbial community composition in a long-term biodiversity experiment at Jena, Germany. We examined responses of bacteria, fungi, archaea, and protists to plant species richness (communities varying from 1 to 60 sown species) and plant FG identity (grasses, legumes, small herbs, tall herbs) in bulk soil. We hypothesized that plant species richness and FG identity would alter microbial community composition and have a positive impact on microbial species richness. Plant species richness had a marginal positive effect on the richness of fungi, but we observed no such effect on bacteria, archaea and protists. Plant species richness also did not have a large impact on microbial community composition. Rather, abiotic soil properties partially explained the community composition of bacteria, fungi, arbuscular mycorrhizal fungi (AMF), archaea and protists. Plant FG richness did not impact microbial community composition; however, plant FG identity was more effective. Bacterial richness was highest in legume plots and lowest in small herb plots, and AMF and archaeal community composition in legume plant communities was distinct from that in communities composed of other plant FGs. We conclude that soil microbial community composition in bulk soil is influenced more by changes in plant FG composition and abiotic soil properties, than by changes in plant species richness per se.

Chronosequencing methanogenic archaea in ancient Longji rice Terraces in China

Chronosequences of ancient rice terraces serve as an invaluable archive for reconstructions of historical human-environment interactions. Presently, however, these reconstructions are based on traditional soil physico-chemical properties. The microorganisms in palaeosols have been unexplored. We hypothesized that microbial information can be used as an additional proxy to complement and consolidate archaeological interpretations. To test this hypothesis, the palaeoenvironmental methanogenic archaeal DNA in Longji Terraces, one of the famous ancient terraces in China, dating back to the late Yuan Dynasty (CE 1361–1406), was chronosequenced by high-throughput sequencing. It was found that the methanogenic archaeal abundance, diversity and community composition were closely associated with the 630years of rice cultivation and in line with changes in multi-proxy data. Particularly, the centennial- and decadal-scale influences of known historical events, including social turbulences (The Taiping Rebellion, CE 1850–1865), palaeoclimate changes (the Little Ice Age) and recorded natural disasters (earthquakes and inundation), on ancient agricultural society were clearly echoed in the microbial archives as variations in alpha and beta diversity. This striking correlation suggests that the microorganisms archived in palaeosols can be quantitatively and qualitatively analyzed to provide an additional proxy, and palaeo-microbial information could be routinely incorporated in the toolkit for archaeological interpretation.

Copper Pollution Increases the Resistance of Soil Archaeal Community to Changes in Water Regime.

Increasing efforts have been devoted to exploring the impact of environmental stresses on soil bacterial communities, but the work on the archaeal community is seldom. Here, we constructed microcosm experiments to investigate the responses of archaeal communities to the subsequent dry-rewetting (DW) disturbance in two contrasting soils (fluvo-aquic and red soil) after 6years of copper pollution. Ten DW cycles were exerted on the two soils with different copper levels, followed by a 6-week recovery period. In both soils, archaeal diversity (Shannon index) in the high copper-level treatments increased over the incubation period, and archaeal community structure changed remarkably as revealed by the non-metric multidimensional scaling ordinations. In both soils, copper pollution altered the response of dominant operational taxonomic units (OTUs) to the DW disturbance. Throughout the incubation and recovery period, the resistance of archaeal abundance to the DW disturbance was higher in the copper-polluted soils than soils without pollution. Taken together, copper pollution altered the response of soil archaeal diversity and community composition to the DW disturbance and increased the resistance of the archaeal abundance. These findings have important implications for understanding soil microbial responses to ongoing environmental change.

Diversity of bacteria and archaea from two shallow marine hydrothermal vents from Vulcano Island.

To obtain new insights into community compositions of hyperthermophilic microorganisms, defined as having optimal growth temperatures of 80°C and above, sediment and water samples were taken from two shallow marine hydrothermal vents (I and II) with temperatures of 100°C at Vulcano Island, Italy. A combinatorial approach of denaturant gradient gel electrophoresis (DGGE) and metagenomic sequencing was used for microbial community analyses of the samples. In addition, enrichment cultures, growing anaerobically on selected polysaccharides such as starch and cellulose, were also analyzed by the combinatorial approach. Our results showed a high abundance of hyperthermophilic archaea, especially in sample II, and a comparable diverse archaeal community composition in both samples. In particular, the strains of the hyperthermophilic anaerobic genera Staphylothermus and Thermococcus, and strains of the aerobic hyperthermophilic genus Aeropyrum, were abundant. Regarding the bacterial community, ε-Proteobacteria, especially the genera Sulfurimonas and Sulfurovum, were highly abundant. The microbial diversity of the enrichment cultures changed significantly by showing a high dominance of archaea, particularly the genera Thermococcus and Palaeococcus, depending on the carbon source and the selected temperature.

Comparison of Archaeal Populations in Soil and Their Encapsulated Iron-Manganese Nodules in Four Locations Spanning from North to South China

ABSTRACTTo characterize the archaeal community composition in soil originating iron-manganese nodules, four types of soils—brown soil, yellow-cinnamon soil, yellow brown soil and red soil—and their associated iron-manganese nodules were collected from Queyu (QY), Zaoyang (ZY), Wuhan (WH) and Guiyang (GY), China, respectively, and subjected to quantitative polymerase chain reaction, cloning and sequencing analyses. The results showed that the archaeal 16S rRNA gene copy numbers in nodules, ranging between 3.59 × 102 and 4.17 × 103 copies g−1 dry nodule, were about 50–1000 times lower than those in their corresponding soils (1.87 × 105 to 1.08 × 106 copies g−1 dry soil), correlating with the low organic matter in the nodules, while archaea accounted for a relatively higher proportion of total prokaryote in nodules than in soils. Community composition analysis suggested that the archaeal diversity in both soils and nodules were much lower than bacterial, but archaeal community structures were similar to each other among the soils and nodules from the same location but varied among four locations, converse to the previous observation that bacterial community shifted markedly between nodules and soils as the result of habitat filtering. The archaeal communities in both soils and nodules were predominated by Thaumarchaeota Group I.1b with the relative abundance ranging between 73.88 and 94.17%, except that Euryarchaeota dominated the archaeal community in one nodule sample (WHn) developed from lake sediment. The finding shed new light on the archaeal diversity and their ecophysiology in different habitats, and further supported the opinion that archaea are more adaptable to stress and unfavorable conditions.

Bacterial, fungal, and plant communities exhibit no biomass or compositional response to two years of simulated nitrogen deposition in a semiarid grassland.

Nitrogen (N) deposition affects myriad aspects of terrestrial ecosystem structure and function, and microbial communities may be particularly sensitive to anthropogenic N inputs. However, our understanding of N deposition effects on microbial communities is far from complete, especially for drylands where data are comparatively rare. To address the need for an improved understanding of dryland biological responses to N deposition, we conducted a two-year fertilization experiment in a semiarid grassland on the Colorado Plateau in the southwestern United States. We evaluated effects of varied levels of N inputs on archaeal, bacterial, fungal and chlorophyte community composition within three microhabitats: biological soil crusts (biocrusts), soil below biocrusts, and the plant rhizosphere. Surprisingly, N addition did not affect the community composition or diversity of any of these microbial groups; however, microbial community composition varied significantly among sampling microhabitats. Further, while plant richness, diversity, and cover showed no response to N addition, there were strong linkages between plant properties and microbial community structure. Overall, these findings highlight the potential for some dryland communities to have limited biotic ability to retain augmented N inputs, possibly leading to large N losses to the atmosphere and to aquatic systems.

Influence of land use on bacterial and archaeal diversity and community structures in three natural ecosystems and one agricultural soil.

Studying shifts in microbial communities under different land use can help in determining the impact of land use on microbial diversity. In this study, we analyzed four different land-use types to determine their bacterial and archaeal diversity and abundance. Three natural ecosystems, that is, wetland (WL), grassland (GL), and forest (FR) soils, and one agricultural soil, that is, tea plantation (TP) soil, were investigated to determine how land use shapes bacterial and archaeal diversity. For this purpose, molecular analyses, such as quantitative polymerase chain reaction (Q-PCR), 16S rRNA gene sequencing, and terminal restriction fragment length polymorphism (T-RFLP), were used. Soil physicochemical properties were determined, and statistical analyses were performed to identify the key factors affecting microbial diversity in these soils. Phylogenetic affiliations determined using the Ribosomal Database Project (RDP) database and T-RFLP revealed that the soils had differing bacterial diversity. WL soil was rich in only Proteobacteria, whereas GR soil was rich in Proteobacteria, followed by Actinobacteria. FR soil had higher abundance of Chloroflexi species than these soils. TP soil was rich in Actinobacteria, followed by Chloroflexi, Acidobacteria, Proteobacteria, and Firmicutes. The archaeal diversity of GL and FR soils was similar in that most of their sequences were closely related to Nitrososphaerales (Thaumarchaeota phylum). In contrast, WL soil, followed by TP soil, had greater archaeal diversity than other soils. Eight different archaeal classes were found in WL soil, and Pacearchaeota class was the richest one. The abundance of bacterial and archaeal 16S rRNA gene copies in WL and GL soils was significantly higher than that in FR and TP soils. Redundancy analysis showed that bacterial diversity was influenced by abiotic factors, e.g., total organic carbon and pH, whereas total nitrogen, pH, and cation exchange capacity (CEC) significantly affected archaeal community composition. Pearson correlation analysis showed that bacterial and archaeal 16S rRNA gene abundance had the highest correlation with clay content (r > 0.905, P < 0.01), followed by total-P, CEC, pH, and silt (%). These results will lead to more comprehensive understanding of how land use affects microbial distribution.