Global biogeography and quantitative seasonal dynamics of Gemmatimonadetes in soil

Bacterial Composition and Survival on Sahara Dust Particles Transported to the European Alps

Deposition of Sahara dust (SD) particles is a frequent phenomenon in Europe, but little is known about the viability and composition of the bacterial community transported with SD. The goal of this study was to characterize SD-associated bacteria transported to the European Alps, deposited and entrapped in snow. During two distinct events in February and May 2014, SD particles were deposited and promptly covered by falling snow, thus preserving them in distinct ochre layers within the snowpack. In June 2014, we collected samples at different depths from a snow profile at the Jungfraujoch (Swiss Alps; 3621 m a.s.l.). After filtration, we performed various microbiological and physicochemical analyses of the snow and dust particles therein that originated in Algeria. Our results show that bacteria survive and are metabolically active after the transport to the European Alps. Using high throughput sequencing, we observed distinct differences in bacterial community composition and structure in SD-layers as compared to clean snow layers. Sporulating bacteria were not enriched in the SD-layers; however, phyla with low abundance such as Gemmatimonadetes and Deinococcus-Thermus appeared to be specific bio-indicators for SD. Since many members of these phyla are known to be adapted to arid oligotrophic environments and UV radiation, they are well suited to survive the harsh conditions of long-range airborne transport.

Long-term oil contamination causes similar changes in microbial communities of two distinct soils

Since total petroleum hydrocarbons (TPH) are toxic and persistent in environments, studying the impact of oil contamination on microbial communities in different soils is vital to oil production engineering, effective soil management and pollution control. This study analyzed the impact of oil contamination on the structure, activity and function in carbon metabolism of microbial communities of Chernozem soil from Daqing oil field and Cinnamon soil from Huabei oil field through both culture-dependent techniques and a culture-independent technique-pyrosequencing. Results revealed that pristine microbial communities in these two soils presented disparate patterns, where Cinnamon soil showed higher abundance of alkane, (polycyclic aromatic hydrocarbons) PAHs and TPH degraders, number of cultivable microbes, bacterial richness, bacterial biodiversity, and stronger microbial activity and function in carbon metabolism than Chernozem soil. It suggested that complicated properties of microbes and soils resulted in the difference in soil microbial patterns. However, the changes of microbial communities caused by oil contamination were similar in respect of two dominant phenomena. Firstly, the microbial community structures were greatly changed, with higher abundance, higher bacterial biodiversity, occurrence of Candidate_division_BRC1 and TAO6, disappearance of BD1-5 and Candidate_division_OD1, dominance of Streptomyces, higher percentage of hydrocarbon-degrading groups, and lower percentage of nitrogen-transforming groups. Secondly, microbial activity and function in carbon metabolism were significantly enhanced. Based on the characteristics of microbial communities in the two soils, appropriate strategy for in situ bioremediation was provided for each oil field. This research underscored the usefulness of combination of culture-dependent techniques and next-generation sequencing techniques both to unravel the microbial patterns and understand the ecological impact of contamination.

Temporal and Spatial Distribution of the Microbial Community of Winogradsky Columns

Winogradsky columns are model microbial ecosystems prepared by adding pond sediment to a clear cylinder with additional supplements and incubated with light. Environmental gradients develop within the column creating diverse niches that allow enrichment of specific bacteria. The enrichment culture can be used to study soil and sediment microbial community structure and function. In this study we used a 16S rRNA gene survey to characterize the microbial community dynamics during Winogradsky column development to determine the rate and extent of change from the source sediment community. Over a period of 60 days, the microbial community changed from the founding pond sediment population: Cyanobacteria, Chloroflexi, Nitrospirae, and Planctomycetes increased in relative abundance over time, while most Proteobacteria decreased in relative abundance. A unique, light-dependent surface biofilm community formed by 60 days that was less diverse and dominated by a few highly abundant bacteria. 67–72% of the surface community was comprised of highly enriched taxa that were rare in the source pond sediment, including the Cyanobacteria Anabaena, a member of the Gemmatimonadetes phylum, and a member of the Chloroflexi class Anaerolinea. This indicates that rare taxa can become abundant under appropriate environmental conditions and supports the hypothesis that rare taxa serve as a microbial seed bank. We also present preliminary findings that suggest that bacteriophages may be active in the Winogradsky community. The dynamics of certain taxa, most notably the Cyanobacteria, showed a bloom-and-decline pattern, consistent with bacteriophage predation as predicted in the kill-the-winner hypothesis. Time-lapse photography also supported the possibility of bacteriophage activity, revealing a pattern of colony clearance similar to formation of viral plaques. The Winogradsky column, a technique developed early in the history of microbial ecology to enrich soil microbes, may therefore be a useful model system to investigate both microbial and viral ecology.

Bacterial Community Features Are Shaped by Geographic Location, Physicochemical Properties, and Oil Contamination of Soil in Main Oil Fields of China

Geographic location and physicochemical properties are thought to represent major factors that shape soil bacterial community abundance and diversity. Crude oil contamination is becoming a notable concern with respect to soil property variation; however, the quantifiable influences of geographic location, physicochemical properties, and oil contamination are still poorly understood. In this study, the 16S ribosomal RNA genes of bacteria in the four oil fields in China were analyzed by using pyrosequencing. Results showed that physicochemical properties were the most dominant factor of bacterial community distribution, followed by geographical location. Oil contamination was a driving factor whose indirect influence was stronger than its direct influence. Under the impact of these three factors, different oil fields presented diversified and distinguishable bacterial community features. The soil of sites with the highest total petroleum hydrocarbon content (HB), nitrogen content (DQ), and phosphorus content (XJ) contained the largest proportion of functional groups participating in hydrocarbon degradation, nitrogen turnover, and phosphorus turnover, respectively. The first dominant phylum of the site with loam soil texture (HB) was Actinobacteria instead of Proteobacteria in other sites with sandy or sandy loam soil texture (DQ, SL, XJ). The site with the highest salinization and alkalization (SL) exhibited the largest proportion of unique local bacteria. The site that was located in the desert with extremely low precipitation (XJ) had the most diversified bacteria distribution. The bacterial community diversity was strongly influenced by soil physicochemical properties.

Bacterial biogeography in the coastal waters of northern Zhejiang, East China Sea is highly controlled by spatially structured environmental gradients

The underlying mechanisms of microbial community assembly in connective coastal environments are unclear. The coastal water area of northern Zhejiang, East China Sea, is a complex marine ecosystem with multiple environmental gradients, where the distributions and determinants of bacterioplankton communities remain unclear. We collected surface water samples from 95 sites across eight zones in this area for investigating bacterial community with 16S rRNA gene high-throughput sequencing. Bacterial alpha-diversity exhibits strong associations with water chemical parameters and latitude, with 75.5% of variation explained by suspended particle. The composition of dominant phyla can group the sampling sites into four bacterial provinces, and most key discriminant phyla and families/genera of each province strongly associate with specific environmental features, suggesting that local environmental conditions shape the biogeographic provincialism of bacterial taxa. At a broader and finer phylogenetic scale, bacterial beta-diversity is dominantly explained by the shared variation of environmental and spatial factors (63.3%); meanwhile, the environmental determinants of bacterial β-diversity generally exhibit spatially structured patterns, suggesting that bacterial assembly in surface water is highly controlled by spatially structured environmental gradients in this area. This study provides evidence for the unique biogeographic pattern of bacterioplankton communities at an entire scale of this marine ecosystem.

Land Use History Shifts In Situ Fungal and Bacterial Successions following Wheat Straw Input into the Soil

Soil microbial communities undergo rapid shifts following modifications in environmental conditions. Although microbial diversity changes may alter soil functioning, the in situ temporal dynamics of microbial diversity is poorly documented. Here, we investigated the response of fungal and bacterial diversity to wheat straw input in a 12-months field experiment and explored whether this response depended on the soil management history (grassland vs. cropland). Seasonal climatic fluctuations had no effect on the diversity of soil communities. Contrastingly fungi and bacteria responded strongly to wheat regardless of the soil history. After straw incorporation, diversity decreased due to the temporary dominance of a subset of copiotrophic populations. While fungi responded as quickly as bacteria, the resilience of fungal diversity lasted much longer, indicating that the relative involvement of each community might change as decomposition progressed. Soil history did not affect the response patterns, but determined the identity of some of the populations stimulated. Most strikingly, the bacteria Burkholderia, Lysobacter and fungi Rhizopus, Fusarium were selectively stimulated. Given the ecological importance of these microbial groups as decomposers and/or plant pathogens, such regulation of the composition of microbial successions by soil history may have important consequences in terms of soil carbon turnover and crop health.

Functional and Structural Succession of Soil Microbial Communities below Decomposing Human Cadavers

The ecological succession of microbes during cadaver decomposition has garnered interest in both basic and applied research contexts (e.g. community assembly and dynamics; forensic indicator of time since death). Yet current understanding of microbial ecology during decomposition is almost entirely based on plant litter. We know very little about microbes recycling carcass-derived organic matter despite the unique decomposition processes. Our objective was to quantify the taxonomic and functional succession of microbial populations in soils below decomposing cadavers, testing the hypotheses that a) periods of increased activity during decomposition are associated with particular taxa; and b) human-associated taxa are introduced to soils, but do not persist outside their host. We collected soils from beneath four cadavers throughout decomposition, and analyzed soil chemistry, microbial activity and bacterial community structure. As expected, decomposition resulted in pulses of soil C and nutrients (particularly ammonia) and stimulated microbial activity. There was no change in total bacterial abundances, however we observed distinct changes in both function and community composition. During active decay (7 - 12 days postmortem), respiration and biomass production rates were high: the community was dominated by Proteobacteria (increased from 15.0 to 26.1% relative abundance) and Firmicutes (increased from 1.0 to 29.0%), with reduced Acidobacteria abundances (decreased from 30.4 to 9.8%). Once decay rates slowed (10 - 23 d postmortem), respiration was elevated, but biomass production rates dropped dramatically; this community with low growth efficiency was dominated by Firmicutes (increased to 50.9%) and other anaerobic taxa. Human-associated bacteria, including the obligately anaerobic Bacteroides, were detected at high concentrations in soil throughout decomposition, up to 198 d postmortem. Our results revealed the pattern of functional and compositional succession in soil microbial communities during decomposition of human-derived organic matter, provided insight into decomposition processes, and identified putative predictor populations for time since death estimation.

Characterization of the microaerophilic, bacteriochlorophyll a-containing bacterium Gemmatimonas phototrophica sp. nov., and emended descriptions of the genus Gemmatimonas and Gemmatimonas aurantiaca

A red-pigmented, bacteriochlorophyll (BChl) a-producing strain, AP64T, was isolated previously from the freshwater Swan Lake located in the western Gobi Desert. Based on its 16S rRNA gene sequence identity (96.1%) to the type strain Gemmatimonas aurantiaca T-27T, the new isolate was tentatively classified as a member of the bacterial phylum Gemmatimonadetes. Here, we report its formal description and polyphasic characterization. Strain AP64T grew best on agar media under 9.8-15.2% atmospheric oxygen. The cells were rods, dividing by symmetrical or asymmetrical binary fission. Budding structures were also observed. Its genomic DNA G+C content was 64.4% (from the draft genome sequence). Phylogenetic analysis based on the 16S rRNA gene sequence clearly separated AP64T from related species. Its genotypic differentiation from phylogenetically close relatives was further supported by performing in silico DNA-DNA hybridization and calculating average nucleotide identity, whereas the high percentage (67.3%) of shared conserved proteins between strain AP64T and Gemmatimonas aurantiaca T-27T supports the classification of the two strains into the same genus. Strain AP64T contained C16 : 1, C14 : 1 and C18 : 1ω9c as predominant fatty acids. The main respiratory quinone was menaquinone 8 (MK-8). The most distinctive feature of strain AP64T was the presence of fully functional purple bacterial photosynthetic reaction centres. The main CO2-fixation pathways were absent. Strain AP64T was capable of growth and BChl production in constant darkness. Thus, strain AP64T is a facultatively photoheterotrophic organism. It represents a novel species of the genus Gemmatimonas, for which the name Gemmatimonasphototrophica sp. nov. is proposed. The type strain is AP64T ( = DSM 29774T = MCCC 1K00454T). Emended descriptions of the genus Gemmatimonas and Gemmatimonas aurantiaca are also provided.

Pyrosequencing reveals changes in soil bacterial communities after conversion of Yungas forests to agriculture

The Southern Andean Yungas in Northwest Argentina constitute one of the main biodiversity hotspots in the world. Considerable changes in land use have taken place in this ecoregion, predominantly related to forest conversion to croplands, inducing losses in above-ground biodiversity and with potential impact on soil microbial communities. In this study, we used high-throughput pyrosequencing of the 16S ribosomal RNA gene to assess whether land-use change and time under agriculture affect the composition and diversity of soil bacterial communities. We selected two areas dedicated to sugarcane and soybean production, comprising both short- and long-term agricultural sites, and used the adjacent native forest soils as a reference. Land-use change altered the composition of bacterial communities, with differences between productive areas despite the similarities between both forests. At the phylum level, only Verrucomicrobia and Firmicutes changed in abundance after deforestation for sugarcane and soybean cropping, respectively. In cultivated soils, Verrucomicrobia decreased sharply (~80%), while Firmicutes were more abundant. Despite the fact that local diversity was increased in sugarcane systems and was not altered by soybean cropping, phylogenetic beta diversity declined along both chronosequences, evidencing a homogenization of soil bacterial communities over time. In spite of the detected alteration in composition and diversity, we found a core microbiome resistant to the disturbances caused by the conversion of forests to cultivated lands and few or none exclusive OTUs for each land-use type. The overall changes in the relative abundance of copiotrophic and oligotrophic taxa may have an impact in soil ecosystem functionality. However, communities with many taxa in common may also share many functional attributes, allowing to maintain at least some soil ecosystem services after forest conversion to croplands.

Ecogenomics reveals metals and land-use pressures on microbial communities in the waterways of a megacity

Networks of engineered waterways are critical in meeting the growing water demands in megacities. To capture and treat rainwater in an energy-efficient manner, approaches can be developed for such networks that use ecological services from microbial communities. Traditionally, engineered waterways were regarded as homogeneous systems with little responsiveness of ecological communities and ensuing processes. This study provides ecogenomics-derived key information to explain the complexity of urban aquatic ecosystems in well-managed watersheds with densely interspersed land-use patterns. Overall, sedimentary microbial communities had higher richness and evenness compared to the suspended communities in water phase. On the basis of PERMANOVA analysis, variation in structure and functions of microbial communities over space within same land-use type was not significant. In contrast, this difference was significant between different land-use types, which had similar chemical profiles. Of the 36 environmental parameters from spatial analysis, only three metals, namely potassium, copper and aluminum significantly explained between 7% and 11% of the variation in taxa and functions, based on distance-based linear models (DistLM). The ecogenomics approach adopted here allows the identification of key drivers of microbial communities and their functions at watershed-scale. These findings can be used to enhance microbial services, which are critical to develop ecologically friendly waterways in rapidly urbanizing environments.

Resuscitation of the rare biosphere contributes to pulses of ecosystem activity

Dormancy is a life history trait that may have important implications for linking microbial communities to the functioning of natural and managed ecosystems. Rapid changes in environmental cues may resuscitate dormant bacteria and create pulses of ecosystem activity. In this study, we used heavy-water (H(18) 2O) stable isotope probing (SIP) to identify fast-growing bacteria that were associated with pulses of trace gasses (CO2, CH4, and N2O) from different ecosystems [agricultural site, grassland, deciduous forest, and coniferous forest (CF)] following a soil-rewetting event. Irrespective of ecosystem type, a large fraction (69-74%) of the bacteria that responded to rewetting were below detection limits in the dry soils. Based on the recovery of sequences, in just a few days, hundreds of rare taxa increased in abundance and in some cases became dominant members of the rewetted communities, especially bacteria belonging to the Sphingomonadaceae, Comamonadaceae, and Oxalobacteraceae. Resuscitation led to dynamic shifts in the rank abundance of taxa that caused previously rare bacteria to comprise nearly 60% of the sequences that were recovered in rewetted communities. This rapid turnover of the bacterial community corresponded with a 5-20-fold increase in the net production of CO2 and up to a 150% reduction in the net production of CH4 from rewetted soils. Results from our study demonstrate that the rare biosphere may account for a large and dynamic fraction of a community that is important for the maintenance of bacterial biodiversity. Moreover, our findings suggest that the resuscitation of rare taxa from seed banks contribute to ecosystem functioning.

Biogeographic patterns of bacterial microdiversity in Arctic deep-sea sediments (HAUSGARTEN, Fram Strait)

Marine bacteria colonizing deep-sea sediments beneath the Arctic ocean, a rapidly changing ecosystem, have been shown to exhibit significant biogeographic patterns along transects spanning tens of kilometers and across water depths of several thousand meters (Jacob et al., 2013). Jacob et al. (2013) adopted what has become a classical view of microbial diversity – based on operational taxonomic units clustered at the 97% sequence identity level of the 16S rRNA gene – and observed a very large microbial community replacement at the HAUSGARTEN Long Term Ecological Research station (Eastern Fram Strait). Here, we revisited these data using the oligotyping approach and aimed to obtain new insight into ecological and biogeographic patterns associated with bacterial microdiversity in marine sediments. We also assessed the level of concordance of these insights with previously obtained results. Variation in oligotype dispersal range, relative abundance, co-occurrence, and taxonomic identity were related to environmental parameters such as water depth, biomass, and sedimentary pigment concentration. This study assesses ecological implications of the new microdiversity-based technique using a well-characterized dataset of high relevance for global change biology.

Restoration of a Mediterranean forest after a fire: bioremediation and rhizoremediation field-scale trial

Forest fires pose a serious threat to countries in the Mediterranean basin, often razing large areas of land each year. After fires, soils are more likely to erode and resilience is inhibited in part by the toxic aromatic hydrocarbons produced during the combustion of cellulose and lignins. In this study, we explored the use of bioremediation and rhizoremediation techniques for soil restoration in a field-scale trial in a protected Mediterranean ecosystem after a controlled fire. Our bioremediation strategy combined the use of Pseudomonas putida strains, indigenous culturable microbes and annual grasses. After 8 months of monitoring soil quality parameters, including the removal of monoaromatic and polycyclic aromatic hydrocarbons as well as vegetation cover, we found that the site had returned to pre-fire status. Microbial population analysis revealed that fires induced changes in the indigenous microbiota and that rhizoremediation favours the recovery of soil microbiota in time. The results obtained in this study indicate that the rhizoremediation strategy could be presented as a viable and cost-effective alternative for the treatment of ecosystems affected by fires.

Adaptation of soil microbial community structure and function to chronic metal contamination at an abandoned Pb-Zn mine

Toxicity of metals released from mine tailings may cause severe damage to ecosystems. A diversity of microorganisms, however, have successfully adapted to such sites. In this study, our objective was to advance the understanding of the indigenous microbial communities of mining-impacted soils. To this end, a metatranscriptomic approach was used to study a heavily metal-contaminated site along a metal concentration gradient (up to 3220 000 and 97 000 mg kg(-1) of Cd, Pb and Zn, respectively) resulting from previous mining. Metal concentration, soil pH and amount of clay were the most important factors determining the structure of soil microbial communities. Interestingly, evenness of the microbial communities, but not its richness, increased with contamination level. Taxa with high metabolic plasticity like Ktedonobacteria and Chloroflexi were found with higher relative abundance in more contaminated samples. However, several taxa belonging to the phyla Actinobacteria and Acidobacteria followed opposite trends in relation to metal pollution. Besides, functional transcripts related to transposition or transfer of genetic material and membrane transport, potentially involved in metal resistance mechanisms, had a higher expression in more contaminated samples. Our results provide an insight into microbial communities in long-term metal-contaminated environments and how they contrast to nearby sites with lower contamination.

Ethyl tert-butyl ether (ETBE)-degrading microbial communities in enrichments from polluted environments

The ethyl tert-butyl ether (ETBE) degradation capacity and phylogenetic composition of five aerobic enrichment cultures with ETBE as the sole carbon and energy source were studied. In all cases, ETBE was entirely degraded to biomass and CO2. Clone libraries of the 16S rRNA gene were prepared from each enrichment. The analyses of the DNA sequences obtained showed different taxonomic compositions with a majority of Proteobacteria in three cases. The two other enrichments have different microbiota with an abundance of Acidobacteria in one case, whereas the microbiota in the second was more diverse (majority of Actinobacteria, Chlorobi and Gemmatimonadetes). Actinobacteria were detected in all five enrichments. Several bacterial strains were isolated from the enrichments and five were capable of degrading ETBE and/or tert-butyl alcohol (TBA), a degradation intermediate. The five included three Rhodococcus sp. (IFP 2040, IFP 2041, IFP 2043), one Betaproteobacteria (IFP 2047) belonging to the Rubrivivax/Leptothrix/Ideonella branch, and one Pseudonocardia sp. (IFP 2050). Quantification of these five strains and two other strains, Rhodococcus sp. IFP 2042 and Bradyrhizobium sp. IFP2049, which had been previously isolated from one of the enrichments was carried out on the different enrichments based on quantitative PCR with specific 16S rRNA gene primers and the results were consistent with the hypothesized role of Actinobacteria and Betaproteobacteria in the degradation of ETBE and the possible role of Bradyrhizobium strains in the degradation of TBA.

Microbial diversity of a Mediterranean soil and its changes after biotransformed dry olive residue amendment

The Mediterranean basin has been identified as a biodiversity hotspot, about whose soil microbial diversity little is known. Intensive land use and aggressive management practices are degrading the soil, with a consequent loss of fertility. The use of organic amendments such as dry olive residue (DOR), a waste produced by a two-phase olive-oil extraction system, has been proposed as an effective way to improve soil properties. However, before its application to soil, DOR needs a pre-treatment, such as by a ligninolytic fungal transformation, e.g. Coriolopsis floccosa. The present study aimed to describe the bacterial and fungal diversity in a Mediterranean soil and to assess the impact of raw DOR (DOR) and C. floccosa-transformed DOR (CORDOR) on function and phylogeny of soil microbial communities after 0, 30 and 60 days. Pyrosequencing of the 16S rRNA gene demonstrated that bacterial diversity was dominated by the phyla Proteobacteria, Acidobacteria, and Actinobacteria, while 28S-rRNA gene data revealed that Ascomycota and Basidiomycota accounted for the majority of phyla in the fungal community. A Biolog EcoPlate experiment showed that DOR and CORDOR amendments decreased functional diversity and altered microbial functional structures. These changes in soil functionality occurred in parallel with those in phylogenetic bacterial and fungal community structures. Some bacterial and fungal groups increased while others decreased depending on the relative abundance of beneficial and toxic substances incorporated with each amendment. In general, DOR was observed to be more disruptive than CORDOR.

Structure, composition and metagenomic profile of soil microbiomes associated to agricultural land use and tillage systems in Argentine Pampas

Agriculture is facing a major challenge nowadays: to increase crop production for food and energy while preserving ecosystem functioning and soil quality. Argentine Pampas is one of the main world producers of crops and one of the main adopters of conservation agriculture. Changes in soil chemical and physical properties of Pampas soils due to different tillage systems have been deeply studied. Still, not much evidence has been reported on the effects of agricultural practices on Pampas soil microbiomes. The aim of our study was to investigate the effects of agricultural land use on community structure, composition and metabolic profiles on soil microbiomes of Argentine Pampas. We also compared the effects associated to conventional practices with the effects of no-tillage systems. Our results confirmed the impact on microbiome structure and composition due to agricultural practices. The phyla Verrucomicrobia, Plactomycetes, Actinobacteria, and Chloroflexi were more abundant in non cultivated soils while Gemmatimonadetes, Nitrospirae and WS3 were more abundant in cultivated soils. Effects on metabolic metagenomic profiles were also observed. The relative abundance of genes assigned to transcription, protein modification, nucleotide transport and metabolism, wall and membrane biogenesis and intracellular trafficking and secretion were higher in cultivated fertilized soils than in non cultivated soils. We also observed significant differences in microbiome structure and taxonomic composition between soils under conventional and no- tillage systems. Overall, our results suggest that agronomical land use and the type of tillage system have induced microbiomes to shift their life-history strategies. Microbiomes of cultivated fertilized soils (i.e. higher nutrient amendment) presented tendencies to copiotrophy while microbiomes of non cultivated homogenous soils appeared to have a more oligotrophic life-style. Additionally, we propose that conventional tillage systems may promote copiotrophy more than no-tillage systems by decreasing soil organic matter stability and therefore increasing nutrient availability.

Functional type 2 photosynthetic reaction centers found in the rare bacterial phylum Gemmatimonadetes

Photosynthetic bacteria emerged on Earth more than 3 Gyr ago. To date, despite a long evolutionary history, species containing (bacterio)chlorophyll-based reaction centers have been reported in only 6 out of more than 30 formally described bacterial phyla: Cyanobacteria, Proteobacteria, Chlorobi, Chloroflexi, Firmicutes, and Acidobacteria. Here we describe a bacteriochlorophyll a-producing isolate AP64 that belongs to the poorly characterized phylum Gemmatimonadetes. This red-pigmented semiaerobic strain was isolated from a freshwater lake in the western Gobi Desert. It contains fully functional type 2 (pheophytin-quinone) photosynthetic reaction centers but does not assimilate inorganic carbon, suggesting that it performs a photoheterotrophic lifestyle. Full genome sequencing revealed the presence of a 42.3-kb-long photosynthesis gene cluster (PGC) in its genome. The organization and phylogeny of its photosynthesis genes suggests an ancient acquisition of PGC via horizontal transfer from purple phototrophic bacteria. The data presented here document that Gemmatimonadetes is the seventh bacterial phylum containing (bacterio)chlorophyll-based phototrophic species. To our knowledge, these data provide the first evidence that (bacterio)chlorophyll-based phototrophy can be transferred between distant bacterial phyla, providing new insights into the evolution of bacterial photosynthesis.

Dynamics of bacterial community succession in a salt marsh chronosequence: evidences for temporal niche partitioning

The mechanisms underlying community assembly and promoting temporal succession are often overlooked in microbial ecology. Here, we studied an undisturbed salt marsh chronosequence, spanning over a century of ecosystem development, to understand bacterial succession in soil. We used 16S rRNA gene-based quantitative PCR to determine bacterial abundance and multitag 454 pyrosequencing for community composition and diversity analyses. Despite 10-fold lower 16S rRNA gene abundances, the initial stages of soil development held higher phylogenetic diversities than the soil at late succession. Temporal variations in phylogenetic β-diversity were greater at initial stages of soil development, possibly as a result of the great dynamism imposed by the daily influence of the tide, promoting high immigration rates. Allogenic succession of bacterial communities was mostly driven by shifts in the soil physical structure, as well as variations in pH and salinity, which collectively explained 84.5% of the variation concerning community assemblage. The community assembly data for each successional stage were integrated into a network co-occurrence analysis, revealing higher complexity at initial stages, coinciding with great dynamism in turnover and environmental variability. Contrary to a spatial niche-based perspective of bacterial community assembly, we suggest temporal niche partitioning as the dominant mechanism of assembly (promoting more phylotype co-occurrence) in the initial stages of succession, where continuous environmental change results in the existence of multiple niches over short periods of time.

Genome Sequence and Methylome of Soil Bacterium Gemmatirosa kalamazoonensis KBS708T, a Member of the Rarely Cultivated Gemmatimonadetes Phylum

Bacteria belonging to the phylum Gemmatimonadetes are found in a wide variety of environments and are particularly abundant in soils. Here, we present the complete genome sequence and methylation pattern of the newly described Gemmatirosa kalamazoonensis type strain.

Microbial community diversities and taxa abundances in soils along a seven-year gradient of potato monoculture using high throughput pyrosequencing approach

BACKGROUND

Previous studies have focused on linking soil community structure, diversity, or specific taxa to disturbances. Relatively little attention has been directed to crop monoculture soils, particularly potato monoculture. Information about microbial community changes over time between monoculture and non-monoculture treatments is lacking. Furthermore, few studies have examined microbial communities in potato monoculture soils using a high throughput pyrosequencing approach.

METHODOLOGY/PRINCIPAL FINDINGS

Soils along a seven-year gradient of potato monoculture were collected and microbial communities were characterized using high throughput pyrosequencing approach. Principal findings are as follows. First, diversity (H(Shannon)) and richness (S(Chao1)) indices of bacterial community, but not of fungal community, were linearly decreased over time and corresponded to a decline of soil sustainability represented by yield decline and disease incidence increase. Second, Fusarium, the only soilborne pathogen-associated fungal genus substantially detected, was linearly increased over time in abundance and was closely associated with yield decline. Third, Fusarium abundance was negatively correlated with soil organic matter (OM) and total nitrogen (TN) but positively with electrical conductivity (EC). Fourth, Fusarium was correlated in abundances with 6 bacterial taxa over time.

CONCLUSIONS

Soil bacterial and fungal communities exhibited differential responses to the potato monoculture. The overall soil bacterial communities were shaped by potato monoculture. Fusarium was the only soilborne pathogen-associated genus associated with disease incidence increase and yield decline. The changes of soil OM, TN and EC were responsible for Fusarium enrichment, in addition to selections by the monoculture crop. Acidobacteria and Nitrospirae were linearly decreased over time in abundance, corresponding to the decrease of OM, suggesting their similar ecophysiologial trait. Correlations between abundance of Fusarium with several other bacterial taxa suggested their similar behaviors in responses to potato monoculture and/or soil variables, providing insights into the ecological behaviors of these taxa in the environment.

Linking geology and microbiology: inactive pockmarks affect sediment microbial community structure

Pockmarks are geological features that are found on the bottom of lakes and oceans all over the globe. Some are active, seeping oil or methane, while others are inactive. Active pockmarks are well studied since they harbor specialized microbial communities that proliferate on the seeping compounds. Such communities are not found in inactive pockmarks. Interestingly, inactive pockmarks are known to have different macrofaunal communities compared to the surrounding sediments. It is undetermined what the microbial composition of inactive pockmarks is and if it shows a similar pattern as the macrofauna. The Norwegian Oslofjord contains many inactive pockmarks and they are well suited to study the influence of these geological features on the microbial community in the sediment. Here we present a detailed analysis of the microbial communities found in three inactive pockmarks and two control samples at two core depth intervals. The communities were analyzed using high-throughput amplicon sequencing of the 16S rRNA V3 region. Microbial communities of surface pockmark sediments were indistinguishable from communities found in the surrounding seabed. In contrast, pockmark communities at 40 cm sediment depth had a significantly different community structure from normal sediments at the same depth. Statistical analysis of chemical variables indicated significant differences in the concentrations of total carbon and non-particulate organic carbon between 40 cm pockmarks and reference sample sediments. We discuss these results in comparison with the taxonomic classification of the OTUs identified in our samples. Our results indicate that microbial communities at the sediment surface are affected by the water column, while the deeper (40 cm) sediment communities are affected by local conditions within the sediment.

Host-specificity and dynamics in bacterial communities associated with Bloom-forming freshwater phytoplankton

Many freshwater phytoplankton species have the potential to form transient nuisance blooms that affect water quality and other aquatic biota. Heterotrophic bacteria can influence such blooms via nutrient regeneration but also via antagonism and other biotic interactions. We studied the composition of bacterial communities associated with three bloom-forming freshwater phytoplankton species, the diatom Aulacoseira granulata and the cyanobacteria Microcystis aeruginosa and Cylindrospermopsis raciborskii. Experimental cultures incubated with and without lake bacteria were sampled in three different growth phases and bacterial community composition was assessed by 454-Pyrosequencing of 16S rRNA gene amplicons. Betaproteobacteria were dominant in all cultures inoculated with lake bacteria, but decreased during the experiment. In contrast, Alphaproteobacteria, which made up the second most abundant class of bacteria, increased overall during the course of the experiment. Other bacterial classes responded in contrasting ways to the experimental incubations causing significantly different bacterial communities to develop in response to host phytoplankton species, growth phase and between attached and free-living fractions. Differences in bacterial community composition between cyanobacteria and diatom cultures were greater than between the two cyanobacteria. Despite the significance, major differences between phytoplankton cultures were in the proportion of the OTUs rather than in the absence or presence of specific taxa. Different phytoplankton species favoring different bacterial communities may have important consequences for the fate of organic matter in systems where these bloom forming species occur. The dynamics and development of transient blooms may also be affected as bacterial communities seem to influence phytoplankton species growth in contrasting ways.

Bacterial community variations in an alfalfa-rice rotation system revealed by 16S rRNA gene 454-pyrosequencing

Crop rotation is a practice harmonized with the sustainable rice production. Nevertheless, the implications of this empirical practice are not well characterized, mainly in relation to the bacterial community composition and structure. In this study, the bacterial communities of two adjacent paddy fields in the 3rd and 4th year of the crop rotation cycle and of a nonseeded subplot were characterized before rice seeding and after harvesting, using 454-pyrosequencing of the 16S rRNA gene. Although the phyla Acidobacteria, Proteobacteria, Chloroflexi, Actinobacteria and Bacteroidetes predominated in all the samples, there were variations in relative abundance of these groups. Samples from the 3rd and 4th years of the crop rotation differed on the higher abundance of groups of presumable aerobic bacteria and of presumable anaerobic and acidobacterial groups, respectively. Members of the phylum Nitrospira were more abundant after rice harvest than in the previously sampled period. Rice cropping was positively correlated with the abundance of members of the orders Acidobacteriales and 'Solibacterales' and negatively with lineages such as Chloroflexi 'Ellin6529'. Studies like this contribute to understand variations occurring in the microbial communities in soils under sustainable rice production, based on real-world data.

Changes and recovery of soil bacterial communities influenced by biological soil disinfestation as compared with chloropicrin-treatment

Soil bacterial composition, as influenced by biological soil disinfestation (BSD) associated with biomass incorporation was investigated to observe the effects of the treatment on the changes and recovery of the microbial community in a commercial greenhouse setting. Chloropicrin (CP) was also used for soil disinfestation to compare with the effects of BSD. The fusarium wilt disease incidence of spinach cultivated in the BSD- and CP-treated plots was reduced as compared with that in the untreated control plots, showing effectiveness of both methods to suppress the disease. The clone library analyses based on 16S rRNA gene sequences showed that members of the Firmicutes became dominant in the soil bacterial community after the BSD-treatment. Clone groups related to the species in the class Clostridia, such as Clostridium saccharobutylicum, Clostridium tetanomorphum, Clostridium cylindrosporum, Oxobacter pfennigii, etc., as well as Bacillus niacini in the class Bacilli were recognized as the most dominant members in the community. For the CP-treated soil, clones affiliated with the Bacilli related to acid-tolerant or thermophilic bacteria such as Tuberibacillus calidus, Sporolactobacillus laevolacticus, Pullulanibacillus naganoensis, Alicyclobacillus pomorum, etc. were detected as the major groups. The clone library analysis for the soil samples collected after spinach cultivation revealed that most of bacterial groups present in the original soil belonging to the phyla Proteobacteria, Acidobacteria, Bacteroidetes, Gemmatimonadetes, Planctomycetes, TM7, etc. were recovered in the BSD-treated soil. For the CP-treated soil, the recovery of the bacterial groups belonging to the above phyla was also noted, but some major clone groups recognized in the original soil did not recover fully.

Proteogenomic analysis of a thermophilic bacterial consortium adapted to deconstruct switchgrass

Thermophilic bacteria are a potential source of enzymes for the deconstruction of lignocellulosic biomass. However, the complement of proteins used to deconstruct biomass and the specific roles of different microbial groups in thermophilic biomass deconstruction are not well-explored. Here we report on the metagenomic and proteogenomic analyses of a compost-derived bacterial consortium adapted to switchgrass at elevated temperature with high levels of glycoside hydrolase activities. Near-complete genomes were reconstructed for the most abundant populations, which included composite genomes for populations closely related to sequenced strains of Thermus thermophilus and Rhodothermus marinus, and for novel populations that are related to thermophilic Paenibacilli and an uncultivated subdivision of the little-studied Gemmatimonadetes phylum. Partial genomes were also reconstructed for a number of lower abundance thermophilic Chloroflexi populations. Identification of genes for lignocellulose processing and metabolic reconstructions suggested Rhodothermus, Paenibacillus and Gemmatimonadetes as key groups for deconstructing biomass, and Thermus as a group that may primarily metabolize low molecular weight compounds. Mass spectrometry-based proteomic analysis of the consortium was used to identify >3000 proteins in fractionated samples from the cultures, and confirmed the importance of Paenibacillus and Gemmatimonadetes to biomass deconstruction. These studies also indicate that there are unexplored proteins with important roles in bacterial lignocellulose deconstruction.

Changes in soil bacterial community structure with increasing disturbance frequency

Little is known of the responsiveness of soil bacterial community structure to disturbance. In this study, we subjected a soil microcosm to physical disturbance, sterilizing 90 % of the soil volume each time, at a range of frequencies. We analysed the bacterial community structure using 454 pyrosequencing of the 16S rRNA gene. Bacterial diversity was found to decline with the increasing disturbance frequencies. Total bacterial abundance was, however, higher at intermediate and high disturbance frequencies, compared to low and no-disturbance treatments. Changing disturbance frequency also led to changes in community composition, with changes in overall species composition and some groups becoming abundant at the expense of others. Some phylogenetic groups were found to be relatively more disturbance-sensitive or tolerant than others. With increasing disturbance frequency, phylogenetic species variability (an index of community composition) itself became more variable from one sample to another, suggesting a greater role of chance in community composition. Compared to the tightly clustered community of the original undisturbed soil, in all the aged disturbed soils the lists of most abundant operational taxonomic units (OTUs) in each replicate were very different, suggesting a possible role of stochasticity in resource colonization and exploitation in the aged and disturbed soils. For example, colonization may be affected by whichever localized concentrations of bacterial populations happen to survive the last disturbance and be reincorporated in abundance into each pot. Overall, it appears that the soil bacterial community is very sensitive to physical disturbance, losing diversity, and that certain groups have identifiable 'high disturbance' vs. 'low disturbance' niches.

Temporal variability in soil microbial communities across land-use types

Although numerous studies have investigated changes in soil microbial communities across space, questions about the temporal variability in these communities and how this variability compares across soils have received far less attention. We collected soils on a monthly basis (May to November) from replicated plots representing three land-use types (conventional and reduced-input row crop agricultural plots and early successional grasslands) maintained at a research site in Michigan, USA. Using barcoded pyrosequencing of the 16S rRNA gene, we found that the agricultural and early successional land uses harbored unique soil bacterial communities that exhibited distinct temporal patterns. α-Diversity, the numbers of taxa or lineages, was significantly influenced by the sampling month with the temporal variability in α-diversity exceeding the variability between land-use types. In contrast, differences in community composition across land-use types were reasonably constant across the 7-month period, suggesting that the time of sampling is less important when assessing β-diversity patterns. Communities in the agricultural soils were most variable over time and the changes were significantly correlated with soil moisture and temperature. Temporal shifts in bacterial community composition within the successional grassland plots were less predictable and are likely a product of complex interactions between the soil environment and the more diverse plant community. Temporal variability needs to be carefully assessed when comparing microbial diversity across soil types and the temporal patterns in microbial community structure can not necessarily be generalized across land uses, even if those soils are exposed to the same climatic conditions.

Organic layer serves as a hotspot of microbial activity and abundance in Arctic tundra soils

Tundra ecosystem is of importance for its high accumulation of organic carbon and vulnerability to future climate change. Microorganisms play a key role in carbon dynamics of the tundra ecosystem by mineralizing organic carbon. We assessed both ecosystem process rates and community structure of Bacteria, Archaea, and Fungi in different soil layers (surface organic layer and subsurface mineral soil) in an Arctic soil ecosystem located at Spitsbergen, Svalbard during the summer of 2008 by using biochemical and molecular analyses, such as enzymatic assay, terminal restriction fragment length polymorphism (T-RFLP), quantitative polymerase chain reaction (qPCR), and pyrosequencing. Activity of hydrolytic enzymes showed difference according to soil type. For all three microbial communities, the average gene copy number did not significantly differ between soil types. However, archaeal diversities appeared to differ according to soil type, whereas bacterial and fungal diversity indices did not show any variation. Correlation analysis between biogeochemical and microbial parameters exhibited a discriminating pattern according to microbial or soil types. Analysis of the microbial community structure showed that bacterial and archaeal communities have different profiles with unique phylotypes in terms of soil types. Water content and hydrolytic enzymes were found to be related with the structure of bacterial and archaeal communities, whereas soil organic matter (SOM) and total organic carbon (TOC) were related with bacterial communities. The overall results of this study indicate that microbial enzyme activity were generally higher in the organic layer than in mineral soils and that bacterial and archaeal communities differed between the organic layer and mineral soils in the Arctic region. Compared to mineral soil, peat-covered organic layer may represent a hotspot for secondary productivity and nutrient cycling in this ecosystem.

Bacterial diversity of the rock-water interface in an East Antarctic freshwater ecosystem, Lake Tawani(P)†

Schirmacher Oasis is one of the few ice-free plateaus in East Antarctica that maintains a unique distribution of over 120 microbial-rich, dynamic freshwater lakes, most of which are unexplored. In this study, we describe the bacterial diversity of the rock-water interface in Lake Tawani(P) using culture-independent Bacterial Tag Encoded FLX Amplicon Pyrosequencing (bTEFAP), clone library construction, and culture-based analysis targeting the eubacterial 16S rRNA gene. Lake Tawani(P)was formed in a fossil valley by the accumulation of snow and glacial melt through surface channels into a low-catchment depression. Overall this lake exhibited thirteen bacterial phyla and one-hundred and twelve genera. The Qiime bioinformatics analysis on the bTEFAP alone exhibited higher coverage of the bacterial composition in Lake Tawani(P) than the clone library construction or culture-based methodology. Particularly due to the higher sensitivity of the bTEFAP approach, we detected and differentiated members of the phyla: Chloroflexi, Gemmatimonadetes, Planctomycetes, Nitrospira, and Candidate Division TM7 that other methods were unable to reveal. Nevertheless we found that the use of multiple approaches identified a more complete bacterial community than by using any single approach. Investigating the bacterial diversity of the Schirmacher Oasis lakes, especially those connected through surface channels and encompassed by valleys, will help unravel the dynamic nature of these unique seasonal, freshwater lakes, which potentially harbors highly adapted bacterial taxa with defined ecological functions.