Prokaryotic Community Composition Research Articles

Disentangling the mechanisms shaping the surface ocean microbiota

BackgroundThe ocean microbiota modulates global biogeochemical cycles and changes in its configuration may have large-scale consequences. Yet, the underlying ecological mechanisms structuring it are unclear. Here, we investigate how fundamental ecological mechanisms (selection, dispersal and ecological drift) shape the smallest members of the tropical and subtropical surface-ocean microbiota: prokaryotes and minute eukaryotes (picoeukaryotes). Furthermore, we investigate the agents exerting abiotic selection on this assemblage as well as the spatial patterns emerging from the action of ecological mechanisms. To explore this, we analysed the composition of surface-ocean prokaryotic and picoeukaryotic communities using DNA-sequence data (16S- and 18S-rRNA genes) collected during the circumglobal expeditions Malaspina-2010 and TARA-Oceans.ResultsWe found that the two main components of the tropical and subtropical surface-ocean microbiota, prokaryotes and picoeukaryotes, appear to be structured by different ecological mechanisms. Picoeukaryotic communities were predominantly structured by dispersal-limitation, while prokaryotic counterparts appeared to be shaped by the combined action of dispersal-limitation, selection and drift. Temperature-driven selection appeared as a major factor, out of a few selected factors, influencing species co-occurrence networks in prokaryotes but not in picoeukaryotes, indicating that association patterns may contribute to understand ocean microbiota structure and response to selection. Other measured abiotic variables seemed to have limited selective effects on community structure in the tropical and subtropical ocean. Picoeukaryotes displayed a higher spatial differentiation between communities and a higher distance decay when compared to prokaryotes, consistent with a scenario of higher dispersal limitation in the former after considering environmental heterogeneity. Lastly, random dynamics or drift seemed to have a more important role in structuring prokaryotic communities than picoeukaryotic counterparts.ConclusionsThe differential action of ecological mechanisms seems to cause contrasting biogeography, in the tropical and subtropical ocean, among the smallest surface plankton, prokaryotes and picoeukaryotes. This suggests that the idiosyncrasy of the main constituents of the ocean microbiota should be considered in order to understand its current and future configuration, which is especially relevant in a context of global change, where the reaction of surface ocean plankton to temperature increase is still unclear.8ZJi5SwgFNAgJoQiFLy3zUVideo

Resveratrol affects in vitro rumen fermentation, methane production and prokaryotic community composition in a time- and diet-specific manner.

SummaryThis study aimed to investigate the effect of resveratrol on methane production, rumen fermentation and microbial composition under high‐concentrate (HC) and high‐forage (HF) diets using the in vitro fermentation system. A total of 25 mg of resveratrol was supplemented into 300 mg of either HC or HF diet. Methane production, total volatile fatty acid (VFA) concentration, molar proportion of VFA, metabolites of resveratrol and prokaryotic community composition were measured after 12 and 24 h of in vitro fermentation. Resveratrol reduced methane production (ml per mg of dry matter degraded) by 41% and 60% under both HC and HF diets (P < 0.001), respectively, and this result could be associated with the lower abundance of Methanobrevibacter (P < 0.001) in response to resveratrol. The molar proportion of propionate was significantly higher in the resveratrol group only under the HC diet (P = 0.045). The relative abundance of 10 bacterial genera was affected by the three‐way interaction of treatment, diet and time (P < 0.05). Resveratrol was partly converted to dihydroresveratrol after 24 h of fermentation, and its degradation could be associated with microbes belonging to the order Coriobacteriales. Our results suggest that multiple factors (e.g. diet and time) should be considered in animal experiments to test the effect of polyphenol or other plant extracts on rumen fermentation, methane emission and microbial composition.

Exoenzymes as a Signature of Microbial Response to Marine Environmental Conditions.

Microbial heterotopic metabolism in the ocean is fueled by a supply of essential nutrients acquired via exoenzymes catalyzing depolymerization of high-molecular-weight compounds. Although the rates of activity for a variety of exoenzymes across various marine environments are well established, the factors regulating the production of these exoenzymes, and to some extent their correlation with microbial community composition, are less known. This study focuses on addressing these challenges using a mesocosm experiment that compared a natural seawater microbial community (control) and exposed (to oil) treatment. Exoenzyme activities for β-glucosidase, leucine aminopeptidase (LAP), and lipase were significantly correlated with dissolved nutrient concentrations. We measured correlations between carbon- and nitrogen-acquiring enzymes (β-glucosidase/lipase versus LAP) and found that the correlation of carbon-acquiring enzymes varies with the chemical nature of the available primary carbon source. Notably, a strong correlation between particulate organic carbon and β-glucosidase activity demonstrates their polysaccharide depolymerization in providing the carbon for microbial growth. Last, we show that exoenzyme activity patterns are not necessarily correlated with prokaryotic community composition, suggesting a redundancy of exoenzyme functions among the marine microbial community and substrate availability. This study provides foundational work for linking exoenzyme function with dissolved organic substrate and downstream processes in marine systems.IMPORTANCE Microbes release exoenzymes into the environment to break down complex organic matter and nutrients into simpler forms that can be assimilated and utilized, thereby addressing their cellular carbon, nitrogen, and phosphorus requirements. Despite its importance, the factors associated with the synthesis of exoenzymes are not clearly defined, especially for the marine environment. Here, we found that exoenzymes associated with nitrogen and phosphorus acquisition were strongly correlated with inorganic nutrient levels, while those associated with carbon acquisition depended on the type of organic carbon available. We also show a linear relationship between carbon- and nitrogen-acquiring exoenzymes and a strong correlation between microbial biomass and exoenzymes, highlighting their significance to microbial productivity. Last, we show that changes in microbial community composition are not strongly associated with changes in exoenzyme activity profiles, a finding which reveals a redundancy of exoenzyme activity functions among microbial community. These findings advance our understanding of previously unknown factors associated with exoenzyme production in the marine environment.

Prokaryotic and Viral Community Composition of Freshwater Springs in Florida, USA.

Aquifers, which are essential underground freshwater reservoirs worldwide, are understudied ecosystems that harbor diverse forms of microbial life. This study investigated the abundance and composition of prokaryotic and viral communities in the outflow of five springs across northern Florida, USA, as a proxy of microbial communities found in one of the most productive aquifers in the world, the Floridan aquifer. The average abundances of virus-like particles and prokaryotic cells were slightly lower than those reported from other groundwater systems, ranging from 9.6 × 103 ml-1 to 1.1 × 105 ml-1 and 2.2 × 103 ml-1 to 3.4 × 104 ml-1, respectively. Despite all of the springs being fed by the Floridan aquifer, sequencing of 16S rRNA genes and viral metagenomes (viromes) revealed unique communities in each spring, suggesting that groundwater microbial communities are influenced by land usage in recharge zones. The prokaryotic communities were dominated by Bacteria, and though the most abundant phyla (Proteobacteria, Cyanobacteria, and Bacteroidetes) were found in relatively high abundance across springs, variation was seen at finer taxonomic resolution. The viral sequences were most similar to those described from other aquatic environments. Sequencing resulted in the completion of 58 novel viral genomes representing members of the order Caudovirales as well as prokaryotic and eukaryotic single-stranded DNA (ssDNA) viruses. Sequences similar to those of ssDNA viruses were detected at all spring sites and dominated the identifiable sequences at one spring site, showing that these small viruses merit further investigation in groundwater systems.IMPORTANCE Aquifer systems may hold up to 40% of the total microbial biomass on Earth. However, little is known about the composition of microbial communities within these critical freshwater ecosystems. Here, we took advantage of Florida's first-magnitude springs (the highest spring classification based on water discharge), each discharging at least 246 million liters of water each day from the Floridan aquifer system (FAS), to investigate prokaryotic and viral communities from the aquifer. The FAS serves as a major source of potable water in the Southeastern United States, providing water for large cities and citizens in three states. Unfortunately, the health of the FAS and its associated springs has declined in the past few decades due to nutrient loading, increased urbanization and agricultural activity in aquifer recharge zones, and saltwater intrusion. This is the first study to describe the prokaryotic and viral communities in Florida's first-magnitude springs, providing a baseline against which to compare future ecosystem change.

Domesticated equine species and their derived hybrids differ in their fecal microbiota

BackgroundCompared to horses and ponies, donkeys have increased degradation of dietary fiber. The longer total mean retention time of feed in the donkey gut has been proposed to be the basis of this, because of the increased time available for feed to be acted upon by enzymes and the gut microbiota. However, differences in terms of microbial concentrations and/or community composition in the hindgut may also underpin the increased degradation of fiber in donkeys. Therefore, a study was conducted to assess if differences existed between the fecal microbiota of pony, donkey and hybrids derived from them (i.e. pony × donkey) when fed the same forage diet.ResultsFecal community composition of prokaryotes and anaerobic fungi significantly differed between equine types. The relative abundance of two bacterial genera was significantly higher in donkey compared to both pony and pony x donkey: Lachnoclostridium 10 and ‘probable genus 10’ from the Lachnospiraceae family. The relative abundance of Piromyces was significantly lower in donkey compared to pony × donkey, with pony not significantly differing from either of the other equine types. In contrast, the uncultivated genus SK3 was only found in donkey (4 of the 8 animals). The number of anaerobic fungal OTUs was also significantly higher in donkey than in the other two equine types, with no significant differences found between pony and pony × donkey. Equine types did not significantly differ with respect to prokaryotic alpha diversity, fecal dry matter content or fecal concentrations of bacteria, archaea and anaerobic fungi.ConclusionsDonkey fecal microbiota differed from that of both pony and pony × donkey. These differences related to a higher relative abundance and diversity of taxa with known, or speculated, roles in plant material degradation. These findings are consistent with the previously reported increased fiber degradation in donkeys compared to ponies, and suggest that the hindgut microbiota plays a role. This offers novel opportunities for pony and pony × donkey to extract more energy from dietary fiber via microbial mediated strategies. This could potentially decrease the need for energy dense feeds which are a risk factor for gut-mediated disease.

Geographical location and habitat predict variation in prokaryotic community composition of Suberites diversicolor

PurposeMarine lakes are unique habitats that house diverse assemblages of benthic and planktonic organisms including endemic species. In this study, we aimed to assess to what extent geographical location (Berau versus Papua) and the degree of marine lake connectivity (relatively open versus closed) to the surrounding marine environment structures the prokaryotic community composition of the sponge species Suberites diversicolor.MethodsSponge specimens were sampled in five marine lakes in Borneo and Papua and one open sea habitat in Taiwan.ResultProkaryotic communities of S. diversicolor were dominated by members assigned to the Proteobacteria (particularly Alphaproteobacteria and Gammaproteobacteria) and Cyanobacteria, which together made up from 78 to 87% of sequences in all samples. The dominant operational taxonomic units (OTUs) in most samples, OTUs 1 and 3, were both assigned to the alphaproteobacterial order Rhodospirillales with OTU-1 dominant in the marine lakes of Berau and Papua and OTU-3 in Taiwan. OTU-3 was also largely absent from Papuan samples but present in all Berau samples. Compositionally, S. diversicolor samples clustered according to geographical location with the main axis of variation separating marine lake samples collected in Berau from those collected in Papua and the second axis of variation separating open sea samples collected in Taiwan from all marine lake samples. In addition, our results suggest that the degree of lake connectivity to the open sea also influences prokaryotic composition.ConclusionAlthough previous studies have shown that sponge-associated microbial communities tend to be stable across different geographical and environmental gradients, in the present study, both geography and local environmental conditions were significant predictors of variation in prokaryotic community composition of S. diversicolor.

Minerals play key roles in driving prokaryotic and fungal communities in the surface sediments of the Qinghai-Tibetan lakes.

There is limited knowledge of the relative influences of deterministic and stochastic processes on prokaryotic and fungal communities in lake sediments. In this study, we surveyed the prokaryotic and fungal community compositions and their influencing factors in 23 surface sediments from six lakes on the Qinghai-Tibetan Plateau (QTP) with the use of Illumina sequencing. The results showed the distribution of prokaryotic and fungal communities in the studied QTP lake sediments was shaped by different assembly processes, with prokaryotes primarily governed by variable selection and homogenizing dispersal (accounting for 57.9% and 37.3% of the observed variations) and fungi being mainly regulated by variable selection, non-dominant processes and homogenizing dispersal (38.3%, 43.7% and 13.7%, respectively). Regarding the variable selection, mineralogical variables played key roles in shaping prokaryotic and fungal community structures. Collectively, these findings expand current knowledge concerning the influences of deterministic (e.g. variable selection) and stochastic processes (e.g. homogenizing dispersal and non-dominant processes) on the prokaryotic and fungal distribution in the QTP lakes.

Volatile organic compounds in the salt-lake sediments of the Tibet Plateau influence prokaryotic diversity and community assembly.

Volatile organic compounds (VOCs) are important environmental factors because they supply nutrients for microbial cells and mediate intercellular interactions. However, few studies have focused on the effects of VOCs on prokaryotic diversity and community composition. In this study, we examined the relationship between prokaryotic diversity and community composition and the content of VOCs in salt-lake sediments from the Tibet Plateau using amplicon sequencing of the 16S rRNA gene. Results showed that the alpha-diversity indices (Chao1, Shannon, and Simpson) were generally negatively correlated with the content of 36 VOCs (P < 0.05). The prokaryotic communities were significantly driven by multiple VOCs at the lineage-dependent pattern (P < 0.05). Further analysis indicated that VOCs, including 3-methylpyruvate, biuret, isocitric acid, and stearic acid, jointly explained 37.3% of the variations in prokaryotic communities. Supplemental VOCs-pyruvate, biuret, alanine, and aspartic acid-notably decreased the Chao1 and Shannon indices and significantly assembled co-occurrence networks for the bacterial communities in the saline sediments. Together, these results demonstrated that VOCs play a critical role in the regulation of the diversity, compositions, and network structures of prokaryotic communities in saline sediments.

Fish-processing effluent discharges influenced physicochemical properties and prokaryotic community structure in arid soils from Patagonia

Along the Patagonian coast, there are processing factories of marine products in land that produce fish-processing effluents. The aim of the present study was to assess the physicochemical properties and the prokaryotic community composition of soils receiving fish-processing effluent discharges (effluent site-ES), and to compare them with those of unaltered soils (control site-CS) in the arid Patagonian steppe. We analyzed soil prokaryotic communities (using amplicon-based sequencing of 16S rRNA genes), soil physicochemical properties and fish-processing effluent characteristics. Soil moisture, electrical conductivity (EC), total and inorganic C were significantly higher in ES than in CS (p < .05). Effluent discharges induced a decrease in the total number of operational taxonomic units (OTUs) and in the Shannon diversity index (p = .0009 and .01, respectively) of soil prokaryotic community. Proteobacteria, Actinobacteria and Acidobacteria were the dominant phyla in CS, while ES soil showed a more heterogeneous composition of phyla. Linear discriminant analysis (LDA) effect size (LEfSe) analysis showed that fish-processing effluent discharges promoted an enrichment of Firmicutes and Bacteroidetes, which are active contributors to organic matter mineralization, along with a decrease of oligotrophic phyla such as Acidobacteria, Chloroflexi, Armatimonadetes and Nitrospirae, commonly found in nutrient-poor arid soils. The concentrations of inorganic C and ammonium, the EC and the soil moisture explained 73% of the total variation within the community composition. Due to its salinity and nutrients, fish-processing effluents have potential mainly for native salt-tolerant plant irrigation, however the impacts of soil prokaryotic community shifts over plant growth remain to be determined.

Combined Application of Organic and Inorganic Nitrogen Fertilizers Affects Soil Prokaryotic Communities Compositions

As a fundamental part of the soil ecosystem, prokaryotes are involved in the preservation of soil functions. However, little is known of how the combined application of long-term organic and inorganic nitrogen fertilizer affects the prokaryotic communities’ dynamics at a paddy field. A long-term positioning experiment initiated in 2013 with four treatments (NO: no N fertilizer, CN: 100% urea N with no organic fertilizer, PM: 80% urea N plus 20% N with pig manure, CM: 80% urea N plus 20% N with compost) were applied to detect the differential responses of soil physicochemical properties, and prokaryotic community structure and composition in different fertilization regimes. The results indicated that the long-term combined application of organic and inorganic nitrogen fertilizers altered the physicochemical properties to some extent and, simultaneously, established unique prokaryotic communities. In detail, the treatment of PM and CM significantly increased the content of soil organic carbon (SOC) and total nitrogen (TN) compared to NO. Moreover, a total of 31 indicator taxa were screened across the four treatments by LDA Effect Size (LEfSe) analysis following the principle of the greatest differences, which suggests that these indicator taxa were more sensitive to the fertilization. This research suggested that the combined application of long-term organic and inorganic nitrogen fertilizers not only contributed to the soil’s physicochemical properties but also changed the prokaryotic community composition.

Geographical Isolation, Buried Depth, and Physicochemical Traits Drive the Variation of Species Diversity and Prokaryotic Community in Three Typical Hypersaline Environments.

The prokaryotic community composition, species diversity and the distribution patterns at various taxonomic levels in a salt lake (Chaka salt lake), solar salterns (Taipei saltworks and Dongfang saltworks), and salt mines (Yuanyongjing salt mine, Xiangyan salt mine, and Dinyuan salt mine) were investigated using clone library or Illumina MiSeq sequencing. The clone library approach revealed that the salt lake harbors low species diversity (H’ = 0.98) as compared to the solar saltern (H’ = 4.36) and salt mine (H’ = 3.57). The dominant group in the salt lake is a species from the genus Haloparvum which constitutes about 85% of the total sequences analyzed. The species diversities in salt salterns and salt mines are richer than in the salt lake, and the dominant group is less significant in terms of total percentage. High-throughput sequencing showed that geographical isolation greatly impacted on the microbial community (phyla level) and species diversity (operational taxonomic units (OTUs) level) of salt mines. Species of the genus Natronomonas are found in all three types of environments investigated. In addition, the microbial community and species diversity of different stratums of the salt mine are very similar. Furthermore, species of the genus Halorubrum flourish in the newest stratum of salt mine and have become the dominant group. This study provides some new knowledge on the species diversity and prokaryotic community composition of three typical hypersaline environments.

Characterization of the microbial community composition in Italian Cinta Senese sausages dry-fermented with natural extracts as alternatives to sodium nitrite

Nitrite is widely used in meat products as a multifunctional additive, combining flavour and colour properties with antioxidant and antimicrobial effects. However, nitrite may form reaction products (i.e., nitrosamine) that are potentially carcinogenic to humans. The meat industry, in response to consumers’ demands for nitrite-free products, is seeking natural alternatives to nitrite, such as plant-based extracts.Three types of dry-fermented sausages were manufactured: NIT, containing 30 ppm of sodium nitrite; GSE, containing grape seed extract and olive pomace hydroxytyrosol; and CHE, containing chestnut extract and olive pomace hydroxytyrosol. Next-generation sequencing (NGS) was used to analyse microbial consortia, which were correlated with physical and chemical parameters.The prokaryotic community composition was similar among treatments, with a high relative abundance of Staphylococcus xylosus and Lactobacillus sakei, collectively accounting for 87% of the total community. However, significant differences were observed in both operational taxonomic unit (OTU) presence/absence and relative abundance. Ten genera varied in abundance between treatments. The increase in Lactobacillaceae in CHE may explain the reduced pH levels detected in these samples.In conclusion, NGS analysis showed that the prokaryotic community composition was similar in GSE and NIT, while CHE varied in both the composition and relative abundance of different taxa.

Biocontrol of Bacterial Wilt Disease Through Complex Interaction Between Tomato Plant, Antagonists, the Indigenous Rhizosphere Microbiota, and Ralstonia solanacearum.

Ralstonia solanacearum (biovar2, race3) is the causal agent of bacterial wilt and this quarantine phytopathogen is responsible for massive losses in several commercially important crops. Biological control of this pathogen might become a suitable plant protection measure in areas where R. solanacearum is endemic. Two bacterial strains, Bacillus velezensis (B63) and Pseudomonas fluorescens (P142) with in vitro antagonistic activity toward R. solanacearum (B3B) were tested for rhizosphere competence, efficient biological control of wilt symptoms on greenhouse-grown tomato, and effects on the indigenous rhizosphere prokaryotic communities. The population densities of B3B and the antagonists were estimated in rhizosphere community DNA by selective plating, real-time quantitative PCR, and R. solanacearum-specific fliC PCR-Southern blot hybridization. Moreover, we investigated how the pathogen and/or the antagonists altered the composition of the tomato rhizosphere prokaryotic community by 16S rRNA gene amplicon sequencing. B. velezensis (B63) and P. fluorescens (P142)-inoculated plants showed drastically reduced wilt disease symptoms, accompanied by significantly lower abundance of the B3B population compared to the non-inoculated pathogen control. Pronounced shifts in prokaryotic community compositions were observed in response to the inoculation of B63 or P142 in the presence or absence of the pathogen B3B and numerous dynamic taxa were identified. Confocal laser scanning microscopy (CLSM) visualization of the gfp-tagged antagonist P142 revealed heterogeneous colonization patterns and P142 was detected in lateral roots, root hairs, epidermal cells, and within xylem vessels. Although competitive niche exclusion cannot be excluded, it is more likely that the inoculation of P142 or B63 and the corresponding microbiome shifts primed the plant defense against the pathogen B3B. Both inoculants are promising biological agents for efficient control of R. solanacearum under field conditions.

Zokor disturbances indicated positive soil microbial responses with carbon cycle and mineral encrustation in alpine grassland

The alpine grassland is a fragile ecosystem sensitive to human disturbance; the Qinghai-Tibetan Plateau alpine grassland is an example with large areas that are currently suffering from degradation. Although subterranean mammals (e.g., the plateau zokor, Eospalax baileyi) are thought to contribute to grassland soil and plant degradation, they are native species and play positive roles in the alpine ecosystem as ecosystem engineers. However, little is known about their effect on soil microbial communities. Using Illumina sequencing of the 16S rRNA gene and the internal transcribed spacer 2 (ITS2) regions, we compared soil prokaryotic and fungal community composition and diversity in areas disturbed by plateau zokors during the grassland recovery process. We found an increase in the number of observed operational taxonomic units (OTUs) of soil prokaryotic and fungal microbes, while the community structure of the microbes became significantly divergent. Soil properties, plant cover, and aboveground biomass explained the majority of the changes in microbial communities, suggesting that the changes in soil and plant characteristics mainly regulate the response of soil microbes to zokor disturbance in alpine grasslands. Zokor disturbances result in positive soil microbial responses in phyla with carbon cycle and mineral encrustation associations, suggesting a positive role for soil microbial community functions. Our findings provide novel evidence that zokors are important ecosystem engineers essential for alpine ecosystem functions.

Microbial colonization of microplastics in the Caribbean Sea

AbstractMicroplastics in the ocean function as an artificial microbial reef, with diverse communities of eukaryotic and bacterial microbiota colonizing its surface. It is not well understood if these communities are specific for the type of microplastic on which they develop. Here, we carried out a 6‐week long incubation experiment of six common plastic polymers in Bocas del Toro, Panama. The community composition of prokaryotes based on 16S rRNA gene sequencing data, when judged under a null model analysis, shows that neither plastic polymer type nor time exposed to the environment plays a significant role in shaping biofilm communities. However, the null model analyses of eukaryotic communities based on 18S rRNA gene sequences reveal that they can be significantly influenced by plastic polymer type and time incubated. This was confirmed by scanning electron microscopy, which allowed us to distinguish plastic‐specific diatom communities by the end of the incubation period.

The linkage between methane production activity and prokaryotic community structure in the soil within a shale gas field in China.

Soil methane generation mainly driven by soil prokaryotic microbes can be coupled with the degradation of petroleum hydrocarbons (PHCs); however, the relationship between prokaryotic community structure and methane production activity in soil with the potential risk of PHC contamination is seldom reported. In this study, 3 soil samples (CS-1 to CS-3) in the area nearby an exploratory gas well and 5 soil samples (DC-1 to DC-5) in a drill cutting dump area were obtained from the Fuling shale gas field (Chongqing City, China). Then, the prokaryotic community structure was examined by Illumina Miseq sequencing, and the linkage between soil methane production rate (MPR) and prokaryotic community composition was analyzed. The results indicated that 2 samples (DC-4 and DC-5) collected from the drill cutting dump area had significantly higher MPR than the other samples, and a significant and positive relationship (r = 0.44, P < 0.05) was found between soil MPR and soil organic matter (OM) content. The prokaryotic community composition in the sample (DC-5) with the highest MPR was different from those in the other samples, and soil OM and MPR were the major factors significantly correlated with the prokaryotic community structure in this soil. The samples (DC-4 and DC-5) with higher MPR had a higher relative abundance of Archaea and different archaeal community structures from the other samples, and the MPR was the sole factor significantly correlated with the archaeal genus composition in this soil. Therefore, both the prokaryotic and archaeal community structures are essential in the determination of soil MPR, and the bacterial genus of Saccharibacteria and the archaeal genus of Methanolobus might be the key contributors for methane generation in this soil from the shale gas field.

Prokaryotic community composition and distribution in coastal sediments following a Po river flood event (northern Adriatic Sea, Italy)

The influence of the freshwater runoff on marine prokaryotes has been largelly studied in the pelagic environment, little is known about the effects on the prokaryotes in coastal sediments. We investigated the distribution of benthic prokaryotes in the northern Adriatic Sea, when an extreme Po River flood event determined high heterogeneity along the estuarine salinity gradient (from mainly freshwater to marine). The microbial diversity was assessed by 16S rRNA gene Illumina sequencing, the quantification of the dominant taxa of Bacteria and Archaea by microscopy techniques (CARD-FISH). Our results showed dominance of Bacteria (eight-fold higher) over Archaea, and highlighted Proteobacteria as the most represented phylum, followed by Bacteroidetes. Prokaryotic abundance, quantified by DAPI staining, was mainly affected by sediment characteristics (Total Organic C and Total N contents, and silt fraction). Abundance reached the highest values in sites directly affected by the plume (range 7.3 × 108 - 2.8 × 109 cell g−1). A considerable difference in prokaryotes composition was observed along the salinity gradient, with an increasing presence of freshwater taxa at stations more influenced by the river discharge. CARD-FISH analyses corroborated these findings, showing higher abundance of beta-Proteobacteria and Planctomycetes at stations closest to the river mouths. Nevertheless, a core microbiome (about 10% of the total OTUs) was present across all the study areas, indicating the ability of this assemblage to survive in rather diverse environmental conditions, differently impacted by the river plume. Our results show that the river plume can affect the diversity and distribution patterns of benthic prokaryotes far into the pro-delta, although further investigations are needed in order to understand how the mixing of bacterial communities of different origin might reflect on ecosystem functioning.

Response of prokaryotic communities to extreme precipitation events in an urban coastal lagoon: A case study of Yundang lagoon, China

Increasing extreme precipitation events (EPEs) can induce biogeochemical disturbances in the coastal lagoon ecosystems. Very little is known about the response of prokaryotic communities to such influences, which are the key components mediating the biogeochemical cycling in lagoons. Here 16S rRNA gene amplicon sequencing and high-through quantitative PCR (HT-qPCR) were employed to investigate the distribution of prokaryotic communities and fecal indicator genes in the surface waters of Yundang lagoon, Xiamen, China during EPEs, respectively. Prokaryotic communities from rainwaters, influents (IFs) and effluents (EFs) from a nearby wastewater treatment plant were also characterised. The results indicated a significant variation in the composition of lagoon prokaryotic communities compared with rainwaters, IFs and EFs. Multivariate and phylogenetic signal analyses revealed that environmental filtering, mainly controlled by salinity, was the major ecological process responsible for the temporal succession of lagoon prokaryotic communities during EPEs. Moreover, the pollution indicator taxa (based on amplicon sequencing) and fecal indicator genes (based on HT-qPCR) demonstrated that EPEs may induce sewage overflows and fecal pollution (mainly from humans and dogs), resulting in an increase in the relative abundance of pollution indicator taxa and genes in Yundang lagoon. Network analysis illustrated that the number of network edges and keystone species decreased along the sampling times, implying that EPEs-induced disturbances may affect prokaryotic species associations. Taken together, this study provides an enhanced understanding of the responses of lagoon prokaryotic communities to EPEs-induced disturbances.

Microbial community structure and function in acid mine drainage from Mengzi, Yunnan Province

In order to explore the microbial communities and functions in distinct environments of acid mine drainage (AMD) ecosystem and fully comprehend the patterns of AMD formation and development, high-throughput sequencing technology was used to study the prokaryotic community composition in AMD puddles and surrounding rills in a mining area in Mengzi, Yunnan Province, China. By combining with physicochemical properties of the samples, we distinguished the key factors affecting the community structure and analyzed the environmental functions of the microflora. We discovered that the main phyla in AMD puddles were Euryarchaeota, Proteobacteria (including the class α-, γ- and δ-Proteobacteria), Nitrospirae, Firmicutes, Actinobacteria, and Acidobacteria. Community structure of the AMD puddles apparently differed from that of the surrounding rills. Microbial diversity was significantly positively correlated with pH, whereas the relative abundance of Thermoplasmata was negatively correlated with pH and this class might play a predominant role in community structure. There was high relative abundance of the genus Ferroplasma (6.60%-86.34%) in different samples of AMD puddles. Acidithiobacillus spp. were the major iron- and/or sulfur-oxidizing bacteria in AMD solutions and sediments, whereas relative abundance of the obligate iron-oxidizer Leptospirillum spp. was lower, and Ferrovum spp. were almost only present in the AMD solutions. In addition, acidophilic or acid-tolerant heterotrophic bacteria were widely distributed in the AMD solutions and sediments, which might promote the growth of iron- and/or sulfur-oxidizers and catalyze the oxidative/reductive dissolution of metal ores. Our results suggested that pH significantly impacted the microbial community structure of AMD environment by affecting the microbial diversity and microflora distribution.

Prokaryotic and eukaryotic microbiomes associated with blooms of the ichthyotoxic dinoflagellate Cochlodinium (Margalefidinium) polykrikoides in New York, USA, estuaries.

While harmful algal blooms caused by the ichthyotoxic dinoflagellate, Cochlodinium (Margalefidinium) polykrikoides, are allelopathic and may have unique associations with bacteria, a comprehensive assessment of the planktonic communities associated with these blooms has been lacking. Here, we used high-throughput amplicon sequencing to assess size fractionated (0.2 and 5 μm) bacterial (16S) and phytoplankton assemblages (18S) associated with blooms of C. polykrikoides during recurrent blooms in NY, USA. Over a three-year period, samples were collected inside (‘patch’) and outside (‘non-patch’) dense accumulations of C. polykrikoides to assess the microbiome associated with these blooms. Eukaryotic plankton communities of blooms had significantly lower diversity than non-bloom samples, and non-bloom samples hosted 30 eukaryotic operational taxonomic units (OTUs) not found within blooms, suggesting they may have been allelopathically excluded from blooms. Differential abundance analyses revealed that C. polykrikoides blooms were significantly enriched in dinoflagellates (p<0.001) and the experimental enrichment of C. polykrikoides led to a significant increase in the relative abundance of eight genera of dinoflagellates but a significant decline in other eukaryotic plankton. Amoebophrya co-dominated both within- and near- C. polykrikoides blooms and was more abundant in bloom patches. The core bacterial microbiome of the >0.2μm fraction of blooms was dominated by an uncultured bacterium from the SAR11 clade, while the >5μm size fraction was co-dominated by an uncultured bacterium from Rhodobacteraceae and Coraliomargarita. Two bacterial lineages within the >0.2μm fraction, as well as the Gammaproteobacterium, Halioglobus, from the >5μm fraction were unique to the microbiome of blooms, while there were 154 bacterial OTUs only found in non-bloom waters. Collectively, these findings reveal the unique composition and potential function of eukaryotic and prokaryotic communities associated with C. polykrikoides blooms.