Prokaryotic Richness Research Articles

Biogeography and dynamics of prokaryotic and microeukaryotic community assembly across 2600 km in the coastal and shelf ecosystems of the China Seas

Marine prokaryotes and microeukaryotes are essential components of microbial food webs, and drive the biogeochemical cycling. However, the underlying ecological mechanisms driving prokaryotic and microeukaryotic community assembly in large-scale coastal ecosystems remain unclear. In this study, we studied biogeographic patterns of prokaryotic and microeukaryotic communities in the coastal and shelf ecosystem of the China Seas. Results showed that prokaryotic richness was the highest in the Yangtze River Plume, whereas microeukaryotic richness decreased from south to north. Prokaryotic-microeukaryotic co-occurrence networks display greater complexity in the Yangtze River Plume compared to other regions, potentially indicating higher environmental heterogeneity. Furthermore, the cross-domain networks revealed that prokaryotes were more interconnected with each other than with microeukaryotes or between microeukaryotes, and all hub nodes were bacterial taxa, suggesting that prokaryotes may be more important for sustaining the stability and multifunctionality of coastal ecosystem than microeukaryotes. Variation Partitioning Analysis revealed that approximately equal proportions of environmental, biotic and spatial factors contribute to variations in microbial community composition. Temperature was the primary environmental driver of both prokaryotic and microeukaryotic communities across the China Seas. Additionally, stochastic processes (dispersal limitation) and deterministic processes (homogeneous selection) were two major ecological factors in shaping microeukaryotic and prokaryotic assemblages, respectively, suggesting their different environmental plasticity and evolutionary mechanisms. Overall, these results demonstrate both prokaryotic and microeukaryotic communities displayed a latitude-driven distribution pattern and different assembly mechanisms, improving our understanding of microbial biogeography patterns under global change and anthropogenic activity driven habitat diversification in the coastal and shelf ecosystem.

Unveiling sedimentary microbial communities: Restored mangrove wetlands show higher heterogeneity and network stability than natural ones

Mangrove wetlands, characterized by high biodiversity and crucial ecological functions, have witnessed extensive restoration efforts in China in recent decades. Despite the successful recovery of standing vegetation, the alterations in below-ground microbial communities, vital engines for completing biogeochemical cycles in wetlands, remain poorly understood. Here, the prokaryotic and microeukaryotic communities in restored mangrove forests (RMF) and natural mangrove forests (NMF) in Shenzhen, the world’s first International Mangrove Center in China were investigated and compared. This work aimed to explore an appropriate sampling strategy for sedimentary microbial community biodiversity study and evaluate their heterogeneity and network stability in RMF and NMF. The results revealed that a “broad-coverage and sparse-spot” sampling strategy was conducive to ensuring a sufficient representation of microbial diversity in mangrove wetlands. Significant differences were found in microbial community structures of RMF and NMF, with the relative abundances of Myxococcales and Cerozoa as potential biomarkers, respectively. RMF displayed higher prokaryotic richness, microbial community dissimilarity, and spatial turnover rate compared to those of NMF, indicating greater microbial diversity and spatial heterogeneity in RMF. Meanwhile, the RMF microbial network was characterized by lower complexity but higher modularity, robustness, and the ratio of negative to positive cohesion. These demonstrated that microbiomes were shaped by stability constraints and the RMF microbial network was more stable and resistant to environmental variations than that of NMF. Interestingly, the stability of these microbial networks appeared to depend on the topological roles of key species rather than on their abundance. Overall, this study disclosed a kind of relationship between the aboveground elements of restored and natural mangrove forests and their belowground microbial communities. These findings provide references for comprehensive assessments of biodiversity, stability, and ecological restoration in mangrove ecosystems.

Prokaryotic richness and diversity increased during Holocene glacier retreat and onset of an Antarctic Lake

Knowledge about biodiversity changes during transitions from glacial landscape to lake formation is limited to contemporary studies. Here, we combined analyses of lithology, chronology and geochemistry with sedimentary ancient DNA metabarcoding to assess such transition in maritime Antarctica. We inferred three paleoenvironmental stages covering the Holocene glacier retreat process. From 4900 to 3850 years before the present, we found the lowest prokaryotic richness/diversity, with bacterial taxa indicators associated to soil and terrestrial environments. From 3850 to 2650 years before the present, a higher carbon content, higher Carbon/Nitrogen variability, increased species richness/diversity, and prokaryotic taxa indicators of long-term energy starvation were detected. Finally, from 2650 to 1070 years before the present, we inferred the onset of a genuine lacustrine environment holding stable Carbon/Nitrogen ratios and the highest prokaryotic diversity, with known aquatic bacterial taxa. Our study unveils for the first time the evolution from a glacier-covered to a freshwater lake through a millennial scale.

Soil prokaryotic characterization in response to natural moisture gradient in the temperate grassland ecosystems

Abstract Soil moisture, which is an important factor affecting ecosystem function, can maintain microbial activity and ultimately change the microbial community by altering vegetation diversity and controlling the diffusion and transport of soil nutrients. To explore the effects of soil water content (SWC) on soil prokaryotic community, we established a study area covering a natural soil moisture gradient and subdivided it into high (HW, 4.80 ± 1.18%), medium (MW, 2.17 ± 0.09%) and low water contents (LW, 1.85 ± 0.14%) in the grassland ecosystem along the south shore of Hulun Lake in Inner Mongolia, China. Environmental factors were determined by field surveys and laboratory analyses. Soil prokaryotes were determined by high-throughput sequencing techniques. Vegetation characteristics and soil physicochemical properties had a significant effect on prokaryotic richness diversity, and SWC was the most important factor influencing prokaryotic richness diversity. In the MW, the number of differential prokaryotes was lowest, and prokaryotic microorganisms had the highest diversity and relative abundance at the phylum level, which may reflect less intrinsic variation and higher overall activity of the prokaryotic community in the MW. In addition, HW and LW had lower prokaryotic diversity and relative abundance at the phylum level, and phenotypic predictions for both groups indicated a more tolerant prokaryotic community. In summary, the prokaryotic community responded significantly to the natural moisture gradients in grassland ecosystems along the south shore of Hulun Lake, and both too high and too low soil moisture increased prokaryotic stress resistance.

Crop diversification improves the diversity and network structure of the prokaryotic soil microbiome at conventional nitrogen fertilization

BackgroundSustainable agriculture seeks to optimize the application of nitrogen (N) fertilizers to reduce adverse economic and ecological effects. Crop diversification has been proposed to increase the efficiency of N fertilization. An open question is how the soil microbiome responds to these beneficial practices.MethodsIn a field study we investigated the effects of mineral N fertilizer with a 0-control, a conventional amount of 150 kg N ha−1 and an excessive application of 250 kg N ha−1 on the soil microbiome within a diversified cropping system with oil radish and undersown ryegrass over a period of 2.5 years and a non-diversified control, both in rotation of potato, winter rye and maize.ResultsN-fertilizations and crop rotations altered the pH, but differences were less pronounced with the diversified system. Compared to the crop species and season, N fertilization and crop diversification had less influence on the abundance of soil bacteria, archaea and fungi. The crop diversification showed a much stronger effect on archaeal than on bacterial or fungal abundances, while the microbial carbon use efficiency correlated strongly with bacterial abundance. At the end of the growing seasons, crop diversification increased prokaryotic richness and Shannon diversity in response to N addition, with a greater increase in the conventional N. At conventional N supply, prokaryotic co-occurrence networks revealed a much denser and complex structure in the diversified system.ConclusionsThe diversified cropping system under conventional N application rates showed positive effects on the prokaryotic soil microbiome by increasing their richness, Shannon diversity, and promoting a more elaborated network structure.

Effects of the cessation of fish-processing effluent discharges on the soil microbiome associated with saltbush patches

In the present scenario of global water scarcity, treated wastewater from some industries -such as the fishing industry- is an interesting resource to consider for irrigation purposes. In a previous study in a Patagonian steppe site dominated by the native halophile shrub Atriplex lampa, fish-processing effluent discharges induced soil salinization, changes in the soil prokaryotic community structure and a reduction of its diversity. In this study we aimed to test if a period without effluent discharges allowed the recovery of the microbial community in soils from this Patagonian steppe site, by analyzing the prokaryotic communities of A. lampa patches during the fish-processing effluent discharges and four years after cessation of such discharges (sites ES1 and ES2, respectively). Additionally, we aimed to test if the soil prokaryotic community of A. lampa patches either exposed to effluent discharges (ES2) or from a coastal dune site (Du) share a common core microbiome as a result of their same shrub cover and similar soil salinity. Regarding the comparison between ES1 and ES2, prokaryotic richness estimators (Chao1 and ACE) increased significantly in ES2. In addition, the cessation of effluent discharges induced a rise of Actinobacteria, and a recovery of some oligotrophic phyla, which had decreased during the effluent discharge period. Regarding the comparison between ES2 and Du, the core microbiome in soils associated with A. lampa patches consisted of just a few taxa. Moreover, Du site revealed a signature of dune-specific prokaryotes comprising halotolerant/halophilic microorganisms adapted to marine and intertidal environments, whilst no such signature was observed in ES2. Overall, our results contribute to unraveling the soil prokaryote diversity associated to A. lampa as well as to a better understanding of the microbiomes from saline environments, having valuable implications for a sustainable reuse of fishing industry wastewaters for irrigation.

Zero-valent iron nanoparticles and organic amendment assisted rhizoremediation of mixed contaminated soil using Brassica napus

Soil is one of our most important natural resources. Regrettably, the expansion of human activities has resulted in the degradation of the soil resource due to contamination with a myriad of organic and inorganic compounds. The remediation of mixed contaminated soils, i.e. soils contaminated with both organic compounds and metals, is challenging as it requires actions to simultaneously decrease metal-induced risks and organic contaminant concentrations. Here, we evaluated the effect of the addition of zero-valent iron nanoparticles (nanoremediation) and organic amendments (biostimulation) on the rhizoremediation, using Brassica napus plants, of soil simultaneously contaminated with zinc (2500 mg kg −1 ) and lindane (100 mg kg −1 ). We used a factorial design with three factors (amendment, nZVI, plant) to evaluate the impact of the applied remediation actions on lindane and extractable Zn concentrations, as well as on soil health recovery as manifested by the values of different soil microbial indicators. The studied microbial indicators were not negatively affected by nZVI application. The application of nZVI was the most effective factor regarding the targeted reduction in lindane concentration (51% average reduction in nZVI treated soils). The highest reduction in extractable Zn was achieved in the presence of B. napus , nZVI and organic amendments (99 and 95% reduction in horse manure-amended and sewage sludge-amended soils, respectively). The combination of the three factors led to the highest values of soil microbial indicators (although a significant triple interaction was not observed for all parameters), especially when combined with horse manure amendment: in this case, prokaryotic richness increased by 64%, respiration by 376%, eukaryotic abundance by 333%, and prokaryotic abundance by 437%, compared to untreated soils. The combination of remediation approaches (rhizoremediation with B. napus , nanoremediation with nZVI, biostimulation with organic amendments) can help overcome the limitations of each individual strategy. • The combination of Brassica napus , nZVI and amendments improved soil health. • The combination of B. napus , nZVI and amendments reduced soil extractable Zn. • The application of nZVI led to the highest decrease in soil lindane concentration. • Soil microbial communities were not negatively affected by nZVI application.

Environmental heterogeneity mediated prokaryotic community variations in marine sediments

Marine ecosystems have been heavily affected by environmental changes, which led to shift of prokaryotic diversity and distribution, especially in the Arctic Ocean. However, how environmental changes affect prokaryotic community still unclear. Here, prokaryotic diversity, community composition and spatial distribution patterns in marine sediments from the Bering Sea to the western Arctic Ocean were surveyed. The results indicated that the lowest bacterial and archaeal diversities were observed in the western Arctic Ocean. Moreover, the prokaryotic richness and diversity showed strong correlation (R2=0.31∼0.83, P<0.05) with heavy metals (such as Cu, Zn, Ni and As). The contents of Ni and As represented a range with in which biological effects occur occasionally in the Bering Strait, but concentrations of Cu, Zn, Ni and As in the western Arctic Ocean showed a probable effect range with in which adverse biological effects occasionally or frequently occur. Furthermore, as geographical distance increased archaeal community similarity decreased faster than bacteria. The abundances of Gammaproteobacteria, Firmicutes and Thaumarchaeota significantly increased from the Bering Sea to the western Arctic Ocean. Conversely, much lower abundances of Alphaproteobacteria, Bacteroidetes and Crenarchaeota were observed in the western Arctic Ocean. In addition, all environmental could explain 73.8% and 85.1% bacterial and archaeal variations, respectively. And heavy metals could independently explain 40.3% and 30.4% community variation for archaea and bacteria, respectively. This study emphasized effects of heavy metals on prokaryotic diversities and distribution patterns in marine sediments, which were helpful to deep understand microbial variation under environmental changes.

Topographic attributes override impacts of agronomic practices on prokaryotic community structure

While topography can infer erosion potential, the practice of conventional agronomic management can trigger accelerated erosion and pose major threats to soil assets such as biodiversity. The majority of farmlands in Upper-Eastern Ghana are moderately hilly and highly susceptible to erosion. This study pioneered the comparative and interactive effects of topography and conventional versus conservation agriculture practices (reduced tillage, main crop and cover crop, crop residue retention vs. removal) in treatments amended with 0, 40, and 80 kg ha−1 N on soil physicochemical properties and microbiota. Topography imposed profound shifts in soil physiochemical properties and prokaryotic community structure. Foot-slope soils harbored higher prokaryotic richness and diversity compared to the up-slope. Bacillaceae (28.95%) and anaerobic bacteria increased in relative abundance in foot-slope soils, while Micrococcaceae (25.79%) gained prominence in up-slope soils. The effect of tillage was significant in foot-slope while crop rotation was influential in up-slope soils on structuring the prokaryotic community. The interactive effect of slope × tillage was significant in altering soil physiochemical properties, but not prokaryotic community structure. Variation in prokaryotic community composition was explained by soil physiochemical properties (14.5%), elevation as a proxy for topography (11.3%), and spatial distance (10.8%), but rather weakly overall by agronomic practices. Among the soil physicochemical properties, pH, clay content, total C%, volumetric water content, temperature, cation exchange capacity, and NO3−-N were relevant factors influencing the soil microbiota. Geomorphic and soil edaphic properties appeared to interact and were the primary triggers of variation in soil microbiota and their responses to the range of agronomic practices that incorporated conservation management outcomes.

Salinity and N input drive prokaryotic diversity in soils irrigated with treated effluents from fish-processing industry

Wastewater reuse for irrigation has become an important practice in many countries in the context of global water scarcity. However, knowledge about the potential soil impact of reusing treated fish-processing (TFP) effluents for irrigation is still limited. The aim of this study was to investigate the response of the soil prokaryotic community in general, and the nitrifying taxa in particular, to TFP-effluent irrigation. We analyzed the impacts of irrigation with two effluent dilutions (EF1 and EF2, with electrical conductivities of 2.7 and 6 mS cm−1, respectively) or water (W) as a control on soil chemical properties, dehydrogenase and nitrifying activities, amoA gene abundances of ammonia-oxidizing bacteria (AOB) and archaea (AOA), and soil prokaryotic community structure and diversity. At the end of the irrigation experiment, soil ammonium, nitrate plus nitrite, dehydrogenase and nitrifying activities, soil electrical conductivity (EC), and sodium adsorption ratio (SAR) were significantly higher in TFP-irrigated treatments than in water irrigated controls. Prokaryotic richness and diversity indices followed the pattern W > EF1 > EF2, and negatively correlated with soil EC, SAR, ammonium, nitrate plus nitrite, and total N concentrations. In particular, EF2-irrigation stimulated soil copiotrophic bacteria (e.g. Proteobacteria and Bacteroidetes) to the detriment of oligotrophic members such as Acidobacteria. TFP-effluent irrigation also influenced the relative abundance of the amoA gene of AOB but not that of AOA; and the composition of nitrifying taxa, by inducing a significant increase in OTUs whose closest cultured matches were ‘Candidatus Nitrosocosmicus franklandus’ and Nitrosospira briensis Nsp10. Overall, irrigation with the more diluted effluent (classified as slight to moderate degree of restriction by local regulations) induced a reduction of soil prokaryotic diversity, whereas the less diluted effluent (severe irrigation restriction) promoted the greatest changes in the prokaryotic community due to the increase in soil salinity and N content.

Depth-related variability in viral communities in highly stratified sulfidic mine tailings

BackgroundRecent studies have significantly expanded our knowledge of viral diversity and functions in the environment. Exploring the ecological relationships between viruses, hosts, and the environment is a crucial first step towards a deeper understanding of the complex and dynamic interplays among them.ResultsHere, we obtained extensive 16S rRNA gene amplicon, metagenomics sequencing, and geochemical datasets from different depths of two highly stratified sulfidic mine tailings cores with steep geochemical gradients especially pH, and explored how variations in viral community composition and functions were coupled to the co-existing prokaryotic assemblages and the varying environmental conditions. Our data showed that many viruses in the mine tailings represented novel genera, based on gene-sharing networks. Siphoviridae, Podoviridae, and Myoviridae dominated the classified viruses in the surface tailings and deeper layers. Both viral richness and normalized coverage increased with depth in the tailings cores and were significantly correlated with geochemical properties, for example, pH. Viral richness was also coupled to prokaryotic richness (Pearson’s r = 0.65, P = 0.032). The enrichment of prophages in the surface mine tailings suggested a preference of lysogenic viral lifestyle in more acidic conditions. Community-wide comparative analyses clearly showed that viruses in the surface tailings encoded genes mostly with unknown functions while viruses in the deeper layers contained genes mainly annotated as conventional functions related to metabolism and structure. Notably, significantly abundant assimilatory sulfate reduction genes were identified from the deeper tailings layers and they were widespread in viruses predicted to infect diverse bacterial phyla.ConclusionsOverall, our results revealed a depth-related distribution of viral populations in the extreme and heterogeneous tailings system. The viruses may interact with diverse hosts and dynamic environmental conditions and likely play a role in the functioning of microbial community and modulate sulfur cycles in situ.6mWQNmd-mJVeghGxVjw1eiVideo

Exceptional but vulnerable microbial diversity in coral reef animal surface microbiomes.

Coral reefs host hundreds of thousands of animal species that are increasingly threatened by anthropogenic disturbances. These animals host microbial communities at their surface, playing crucial roles for their fitness. However, the diversity of such microbiomes is mostly described in a few coral species and still poorly defined in other invertebrates and vertebrates. Given the diversity of animal microbiomes, and the diversity of host species inhabiting coral reefs, the contribution of such microbiomes to the total microbial diversity of coral reefs could be important, yet potentially vulnerable to the loss of animal species. Analysis of the surface microbiome from 74 taxa, including teleost fishes, hard and soft corals, crustaceans, echinoderms, bivalves and sponges, revealed that more than 90% of their prokaryotic phylogenetic richness was specific and not recovered in surrounding plankton. Estimate of the total richness associated with coral reef animal surface microbiomes reached up to 2.5% of current estimates of Earth prokaryotic diversity. Therefore, coral reef animal surfaces should be recognized as a hotspot of marine microbial diversity. Loss of the most vulnerable reef animals expected under present-day scenarios of reef degradation would induce an erosion of 28% of the prokaryotic richness, with unknown consequences on coral reef ecosystem functioning.

Cultivating the Macroalgal Holobiont: Effects of Integrated Multi-Trophic Aquaculture on the Microbiome of Ulva rigida (Chlorophyta)

Ulva is a ubiquitous macroalgal genus of commercial interest. Integrated Multi Trophic Aquaculture (IMTA) systems promise large-scale production of macroalgae due to their high productivity and environmental sustainability. Complex host-microbiome interactions play a decisive role in macroalgal development, especially in Ulva spp. due to algal growth- and morphogenesis-promoting factors released by associated bacteria. However, our current understanding of the microbial community assembly and structure in cultivated macroalgae is scant. We aimed to determine (i) to what extent IMTA settings influence the microbiome associated with U. rigida and its rearing water, (ii) to explore the dynamics of beneficial microbes to algal growth and development under IMTA and (iii) to improve current knowledge of host-microbiome interactions. We examined the diversity and taxonomic composition of the prokaryotic communities associated with wild versus IMTA-grown Ulva rigida and surrounding seawater by 16S rRNA gene amplicons. With 3141 Amplicon Sequence Variants (ASVs), the prokaryotic richness was higher in water than in association with U. rigida. Bacterial ASVs were more abundant in aquaculture water samples than water collected from the lagoon. The beta diversity analysis revealed distinct prokaryotic communities associated with Ulva collected in both aquacultures and coastal waters. Aquaculture samples (water and algae) shared 22% of ASVs, whereas natural, coastal lagoon samples only 9%. While cultivated Ulva selected 239 (8%) host-specific ASVs, wild specimens possessed more than twice host-specific ASVs (17%). Cultivated U. rigida specimens enriched the phyla Cyanobacteria, Planctomycetes, Verrucomicrobia, and Proteobacteria. Within the Gammaproteobacteria, while Glaciecola mostly dominated the microbiome in cultivated algae, the genus Granulosicoccus characterized both Ulva microbiomes. In both wild and IMTA settings, the phylum Bacteroidetes was more abundant in the bacterioplankton than in association with U. rigida. However, we observed that the Saprospiraceae family within this phylum was barely present in lagoon water but very abundant in aquaculture water. Aquacultures promoted the presence of known morphogenesis-inducing bacteria in water samples. Our study suggests that IMTA significantly shaped the structure and composition of the microbial community of the rearing water and cultivated U. rigida. Detailed analysis revealed the presence of previously undetected taxa associated with Ulva, possessing potentially unknown functional traits.

Diversity of Bacterial Community in the Oxygen Minimum Zones of Arabian Sea and Bay of Bengal as Deduced by Illumina Sequencing.

The Indian Ocean harbors oxygen minimum zones (OMZs) in the Arabian Sea and Bay of Bengal, with dissolved oxygen < 20 μM, located at the mid-depths of the water column. Till date, high-throughput sequence-data on depth-wise distribution of prokaryotic communities have rarely been reported from these OMZs. The present study aimed to characterize the prokaryotic diversity inhabiting Arabian Sea Time Series (ASTS) and India’s Idea 2 (II2) in the Arabian Sea, and Bay of Bengal Time Series (BoBTS) in the Bay of Bengal OMZs based on amplicon sequencing of 16S rRNA gene regions, along six sampled depths in the water column. High prokaryotic richness was observed in the Arabian Sea and Bay of Bengal samples. Operational taxonomic units (OTUs) in the range of 1249–3298 were identified, wherein, less prokaryotic diversity was observed at surface and within oxygen minimum depths. At phylum level, most OTUs were affiliated to Bacteroidetes, Chloroflexi, Cyanobacteria, Marinimicrobia, Planctomycetes, and Proteobacteria. Prokaryotic community differed between ASTS, II2 and BoBTS locations along varying physicochemical conditions. Predictive functional profiling of the bacterial communities suggested the involvement of abundant microbes in nitrogen and sulfur metabolism pathways. Bacterial isolates belonging to genera from the clades, δ-Proteobacteria and γ-Proteobacteria, described previously for their participation in biogeochemical cycling of N-and-S in the OMZs were reported from deoxygenated waters of both the basins. Bacteria involved in anammox such as Candidatus Scalindua were found to be relatively high at ASTS and II2 locations in the Arabian Sea. Further studies are required to ascertain the role of abundant bacteria along the dynamic oceanographic processes in the OMZs.

The gorgonian coral Eunicella labiata hosts a distinct prokaryotic consortium amenable to cultivation.

Microbial communities inhabiting gorgonian corals are believed to benefit their hosts through nutrient provision and chemical defence; yet much remains to be learned about their phylogenetic uniqueness and cultivability. Here, we determined the prokaryotic community structure and distinctiveness in the gorgonian Eunicella labiata by Illumina sequencing of 16S rRNA genes from gorgonian and seawater metagenomic DNA. Furthermore, we used a 'plate-wash' methodology to compare the phylogenetic diversity of the 'total' gorgonian bacteriome and its 'cultivatable' fraction. With 1016 operational taxonomic units (OTUs), prokaryotic richness was higher in seawater than in E. labiata where 603 OTUs were detected, 68 of which were host-specific. Oceanospirillales and Rhodobacterales predominated in the E. labiata communities. One Oceanospirillales OTU, classified as Endozoicomonas, was particularly dominant, and closest relatives comprised exclusively uncultured clones from other gorgonians. We cultivated a remarkable 62% of the bacterial symbionts inhabiting E. labiata: Ruegeria, Sphingorhabdus, Labrenzia, other unclassified Rhodobacteraceae, Vibrio and Shewanella ranked among the 10 most abundant genera in both the cultivation-independent and dependent samples. In conclusion, the E. labiata microbiome is diverse, distinct from seawater and enriched in (gorgonian)-specific bacterial phylotypes. In contrast to current understanding, many dominant E. labiata symbionts can, indeed, be cultivated.

Response to nitrogen addition reveals metabolic and ecological strategies of soil bacteria

The nitrogen (N) cycle represents one of the most well-studied systems, yet the taxonomic diversity of the organisms that contribute to it is mostly unknown, or linked to poorly characterized microbial groups. While new information has allowed functional groups to be refined, they still rely on a priori knowledge of enzymes involved and the assumption of functional conservation, with little connection to the role the transformations, plays for specific organisms. Here, we use soil microcosms to test the impact of N deposition on prokaryotic communities. By combining chemical, genomic and transcriptomic analysis, we are able to identify and link changes in community structure to specific organisms catalysing given chemical reactions. Urea deposition led to a decrease in prokaryotic richness, and a shift in community composition. This was driven by replacement of stable native populations, which utilize energy from N-linked redox reactions for physiological maintenance, with fast responding populations that use this energy for growth. This model can be used to predict response to N disturbances and allows us to identify putative life strategies of different functional and taxonomic groups, thus providing insights into how they persist in ecosystems by niche differentiation.

Seasonal changes of bacterial and archaeal communities in the dark ocean: Evidence from the Mediterranean Sea

The study site located in the northwestern Mediterranean Sea was visited nine times in 2005–2006 to collect water samples from the epipelagic (5 m), mesopelagic (200 m, 600 m), and bathypelagic (1000 m, 2000 m) zones. The relative abundance of Bacteria, Crenarchaea, and Euryarchaea was determined by catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH). Apparent richness (total number of phylotypes detected) and community composition (different phylotypes detected) of Bacteria and Archaea were assessed by denaturing gradient gel electrophoresis (DGGE) analysis of polymerase chain reaction (PCR)-amplified fragments of the 16S ribosomal ribonucleic acid (rRNA) gene followed by sequencing and phylogenetic analysis of selected phylotypes. The relative abundance of Crenarchaea and Euryarchaea in the epipelagic zone increased as stratification decreased. Apparent bacterial richness increased with decreasing stratification in the mesopelagic and bathypelagic zones. Deep vertical mixing at the study site represented the beginning of a seasonal succession. The effects of this succession were detectable throughout the water column and led to distinct prokaryotic communities in different depth layers during the stratified period. The seasonal variability in the relative abundance of Bacteria, as well as apparent prokaryotic richness and community composition, was comparable between the different depth layers. This suggests that prokaryotic communities of the dark ocean can be as dynamic as those found at the surface.

Relationship of Geographic Distance, Depth, Temperature, and Viruses with Prokaryotic Communities in the Eastern Tropical Atlantic Ocean

The richness and biogeographical distribution pattern of bacterial and archaeal communities was assessed by terminal restriction fragment length polymorphism analysis of polymerase chain reaction-amplified fragments of the 16S rRNA gene at the surface (15-25 m depth), in the deep chlorophyll maximum layer (DCM; 50 m depth), and deep waters (75-1000 m depth) of the eastern tropical Atlantic Ocean. Additionally, prokaryotic and viral abundance and the frequency of infected prokaryotic cells (FIC) were determined along with physico-chemical parameters to identify factors influencing prokaryotic richness and biogeography. Viral abundance was highest in the DCM layer averaging 45.5 x 10(6) ml(-1), whereas in the mixed surface layer and in the waters below the DCM, average viral abundance was 11.3 x 10(6) and 4.3 x 10(6) ml(-1), respectively. The average estimate of FIC was 8.3% in the mixed surface layer and the DCM and 2.4% in deeper waters. FIC was positively related to prokaryotic and viral abundance and negatively to archaeal richness. There was no detectable effect of geographic distance (maximum distance between stations approximately 4600 km) or differences between water masses on bacterial and archaeal community composition. Bacterial communities showed a clear depth zonation, whereas changes in archaeal community composition were related to temperature and FIC. The results indicate that planktonic archaeal virus host systems are a dynamic component of marine ecosystems under natural conditions.

Prokaryotic genetic diversity throughout the salinity gradient of a coastal solar saltern.

Bacterial and archaeal assemblages have been studied in a multipond solar saltern using a range of microbial ecology techniques by four laboratories simultaneously. These include 16S rDNA sequencing from both denaturing gradient gel electrophoresis (DGGE) and clone libraries, and culturing methods. Water samples from eight ponds were analysed, covering a salinity range from near sea water (4% salt) to saturated sodium chloride (37% salt; ponds called crystallizers). Clone libraries focused on ponds with salinity of 8%, 22% and 32%. Although different cloning strategies were able to retrieve the same type of dominant sequences, there were differing degrees of success with less abundant sequences. Thus, the use of two sets of primers recovered a higher number of phylotypes. Bacterial and archaeal isolates were, however, different from any of the retrieved environmental sequences. For Bacteria, most sequences in the 8% salt pond were related to organisms of marine origin. Thus, representatives of the alpha-, beta-, gamma- and epsilon-subdivisions of Proteobacteria, the Cytophaga-Flavobacterium-Bacteroides group (CFB), high-G+C Gram-positive bacteria and cyanobacteria were found. In the 22% salt pond, alpha- and gamma-Proteobacteria, cyanobacteria and CFB were the only groups found, and most of them were related to specialized halophilic bacteria. From the 32% salt pond, only CFB were found, and most of the sequences retrieved clustered with Salinibacter ruber, an extremely halophilic bacterium. A decrease in the richness of bacterial genera was therefore apparent along the gradient. Archaea behaved quite similarly. In the lowest salinity ponds, sequences were related to environmental clones of Marine Archaea Group III (Thermoplasmales relatives) and to unclassified branches of Euryarchaeaota. In the 8%, 22% and 32% ponds, most of the clones were related to different cultured strains of Halobacteriaceae. Finally, most sequences from the crystallizers clustered with the uncultured square archaeon SPhT. Crenarchaeaota were not detected. Despite the fact that higher prokaryotic richness was apparent in the lower salinity ponds than in the crystallizers, the diversity index from clone libraries calculated according to Shannon and Weaver did not show this trend. This was because diversity in the crystallizers can be considered as 'microdiversity', the co-existence of several closely related clones of Bacteria (the S. ruber cluster) and Archaea (the SPhT cluster). Regardless of the changes in abundance, both Bacteria and Archaea showed the same pattern; as salinity increased, the number of different clusters decreased, and only one cluster became dominant. Both clusters, however, showed a considerable degree of microdiversity. The meaning of such microdiversity remains to be determined.