OTU Level Research Articles

Soil fungal community is more sensitive to nitrogen deposition than increased rainfall in a mixed deciduous forest of China

Nitrogen (N) deposition and intensified rainfall can strongly affect soil microbial community, but compared with available studies on bacteria, those on soil fungi are quite limited. Here we carried out a field experiment in a mixed deciduous forest of China to study the influences of increased N deposition and rainfall on soil fungi by using quantitative PCR and high-throughput sequencing method. The results demonstrated that (1) N addition significantly increased fungal abundance and alpha diversity (richness, Shannon index and Invsimpson index), changed fungal community composition at OTU level, and marginally increased the relative abundance of Ascomycota and Zygomycota, while water addition showed no remarkable effects on fungal abundance, biodiversity and community composition. (2) N addition significantly increased the richness of saprotrophic fungi and pathogenic fungi, and the relative abundance of saprotrophic fungi, but water addition only slightly increased the abundance of pathogenic fungi. (3) Fungal composition dissimilarity closely correlated with the disparity of soil parameters as a whole. Soil NH4+-N exhibited strong positive correlation with the richness of pathogenic fungi and mycorrhizal fungi, while both soil moisture and NH4+-N tightly correlated with soil fungal abundance and alpha diversity indices. We concluded that in this N-limited but non-water-limited forest ecosystem, N deposition posed stronger effects on soil fungi than increased rainfall, partially mediated by changes in soil properties.

Difference of soil nematode communities between the humus and soil surface layer in the cold temperate coniferous and broadleaved mixed forest of Yulong Snow Mountain Nature Reserve, Yunnan, China

A high-throughput sequencing approach was used to differentiate the nematode communities in the humus and soil surface layer (0-10 cm) in 20 hm2 plot located in the cold temperate coniferous and broadleaved mixed forest of Yulong Snow Mountain Nature Reserve, Lijiang, Yunnan. A total of 5744582 sequences were obtained, which were further annotated to 44 nematode families. In the humus layer, 37 families were recorded, with Tylenchidae (18.1%) being the most dominant family. For trophic groups, bacterivorous, fungivorous and herbivorous were predominant. The soil surface layer had 41 families, with Mononchidae (45.4%) being the most dominant family. The relative abundance of predatory nematode was highest in the soil surface layer. There was no significant difference in the α diversity indices (Shannon, Simpson and Chao1 index) of nematode communities at the OTU level between two habitats. At the family level, however, α diversity of nematode community in the humus layer was significantly lower than in soil surface layer. β diversity of the nematode community was significantly different in the two habitats, with lower Cody index but high Sorensen non-similarity index in the humus habitat. Results of non-metric multidimensional scaling (NMDS) analysis showed that the internal structure difference of nematode community in the soil surface layer was higher than that in the humus layer.

Characterisation and comparison of the mucosa-associated bacterial communities across the gastrointestinal tract of stranded green turtles, <em>Chelonia mydas</em>

Chelonia mydas are primarily herbivorous long-distance migratory sea turtles that contribute to marine ecosystems. Extensive research has been conducted to restore the populations of green turtles. Little is known about their gut microbiota which plays a vital role in their health. We investigated the mucosa-associated bacterial communities across the gastrointestinal (GI) tract of a total four (3, juvenile and 1, adult) stranded green turtles. Samples taken from four GI regions including oesophagus, stomach, small intestine and large intestine were analysed by high-throughput sequencing targeting hypervariable V1-V3 regions of the bacterial 16S rRNA gene. Bacterial diversity and richness decreased longitudinally along the GI tract from oesophagus to the small intestine of stranded turtles. The large intestine showed a higher bacterial diversity and richness compared to small intestine. The bacterial community of green turtles' GI tract was largely dominated by Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes and Fusobacteria. Aerobic and facultative anaerobic bacteria prevailed primarily in the oesophagus while anaerobes (Lachnospiraceae, Peptostreptococcaceae and Ruminococcaceae) constituted the bulk of large intestinal microbiota. Firmicutes dominated the GI tract except within the small intestine where Proteobacteria prevailed. At the OTU level, six percent of the total OTUs (>1% relative abundance) were common in all GI regions. This is a comprehensive characterisation of bacterial microbiota across the GI tract in green turtles which will provide a reference for future studies on turtle gut microbiome and their metabolism to improve their health and nutrition during rehabilitation.

Temporal Stability of Bacterial Communities in Antarctic Sponges.

Marine sponges host dense, diverse, and species-specific microbial communities around the globe; however, most of the current knowledge is restricted to species from tropical and temperate waters. Only recently, some studies have assessed the microbiome of a few Antarctic sponges; however, contrary to low mid-latitude sponges, the knowledge about temporal (stability) patterns in the bacterial communities of Antarctic sponges is absent. Here, we studied the temporal patterns of bacterial communities in the Antarctic sponges Mycale (Oxymycale) acerata, Isodictya sp., Hymeniacidon torquata, and Tedania (Tedaniopsis) wellsae that were tagged in situ and monitored during three austral summers over a 24-month period. By using amplicon sequencing of the bacterial 16S rRNA gene we found that the microbiome differed between species. In general, bacterial communities were dominated by gammaproteobacterial OTUs; however, M. acerata showed the most distinct pattern, being dominated by a single betaproteobacterial OTU. The analysis at OTU level (defined at 97% sequence similarity) showed a highly stable bacterial community through time, despite the abnormal seawater temperatures (reaching 3°C) and rates of temperature increase of 0.15°C day–1 recorded in austral summer 2017. Sponges were characterized by a small core bacterial community that accounted for a high percentage of the abundance. Overall, no consistent changes in core OTU abundance were recorded for all studied species, confirming a high temporal stability of the microbiome. In addition, predicted functional pathway profiles showed that the most abundant pathways among all sponges belonged mostly to metabolism pathway groups (e.g., amino acid, carbohydrate, energy, and nucleotide). The predicted functional pathway patterns differed among the four sponge species. However, no clear temporal differences were detected supporting what was found in terms of the relatively stable composition of the bacterial communities.

Responses of the rhizosphere bacterial community in acidic crop soil to pH: Changes in diversity, composition, interaction, and function

Soil pH is an important predictor of bacterial community composition and diversity. Examining the effects of pH on diversity, structure, interaction, and function of rhizosphere bacterial communities in acidic crop soils provide valuable information for knowing potential role of rhizosphere bacteria in crop yield. Here, we collected soils from artificial greenhouses and applied Illumina Miseq sequencing, quantitative PCR techniques, multiple ecological analysis methods, including topological analysis and functional profiling to analyze our data and validate our hypotheses. We found that the soil physicochemical properties, species diversity, and rhizosphere bacterial community composition were significantly affected by the degree of soil acidification (pH < 5.5 and pH > 5.5) but not vegetation type. Additionally, bacterial absolute abundance increased with higher pH. The 18 soil samples were clustered into two distinct groups of pH < 5.5 and pH > 5.5 at the OTU level, and soil pH had more of an effect on bacterial community composition compared to the other physicochemical variables. In addition, rhizosphere bacteria might presented relatively less competition for survival in pH < 5.5 soils, and bacterial community functions, including nutrient (i.e., carbon, nitrogen, phosphorus, and sulphur) cycling-related enzymes and proteins, were downregulated in more acidic soils (pH < 5.5) based on sequence analysis. To our knowledge, this report is the first to show that pH is a key factor affecting the diversity, structure, interaction, and function of rhizosphere bacterial communities in acidic crop soil in artificial greenhouses. Our findings emphasize that community function and structure of rhizosphere bacteria are closely correlated in more acidic soils, and the decreased crop yield may be correlated with attenuation of the function of the rhizosphere bacterial community.

Historical Drought Affects Microbial Population Dynamics and Activity During Soil Drying and Re-Wet

A history of drought exposure promoted by variable precipitation regimes can select for drought-tolerant soil microbial taxa, but the mechanisms of survival and death of microbial populations through the selective stresses of soil drying and re-wet are not well understood. We subjected soils collected from a 15-year field drought experiment ("Altered" precipitation historywith extended dry periods,versus the "Ambient" field control) to a laboratory drying/re-wetting experiment, to learn whether selective population survival, death, or maintenance of protein synthesis potential and microbial respirationthrough variable soil water conditions was affected by field drought legacy. Microbial community composition, as measured by Illumina MiSeq sequencing of the 16S rRNA and 16S rRNA gene, shifted with laboratory drying/re-wet and field drought treatments. In Ambient soils, there was a higher proportion of reduced OTU abundance (indicative of mortality) during re-wet, whereas Altered soils had a greater proportion of stable OTU populations that did not change in abundance (indicative ofsurvival) through drying/re-wet. Altered soils alsohad a lower proportion of rRNA:rRNA genes (lower protein synthesis potential) during dry-down, a greater weighted mean rRNA operon number (potential growth rate and r-selection) which was associated with higher abundance of Firmicutes (order Bacillales), and lower average microbial respiration rates. These data demonstrate that soils with a weaker historical drought legacy exhibit a higher prevalence of microbial water-stress mortality and differential survival and death at OTU levels following short-term dryingand re-wetting, concurrent with higher carbon loss potential. This work provides novel insight into the mechanisms and consequencesof soil microbial changes resulting fromextended drought conditions.

Microdiversity ensures the maintenance of functional microbial communities under changing environmental conditions.

Microdiversity can lead to different ecotypes within the same species. These are assumed to provide stability in time and space to those species. However, the role of microdiversity in the stability of wholemicrobial communities remains underexplored. Understanding the drivers of microbial community stability is necessary to predict community response to future disturbances. Here, we analyzed 16S rRNA gene amplicons from eight different temperate bog lakes at the 97% OTU and amplicon sequence variant (ASV) levels and found ecotypes within the same OTU with different distribution patterns in space and time. We observed that these ecotypes are adapted to different values of environmental factors such as water temperature and oxygen concentration. Our results showed that the existence of several ASVs within a OTU favored its persistence across changing environmental conditions. We propose that microdiversity aids the stability of microbial communities in the face of fluctuations in environmental factors.

93 Host genetics help shape the rumen microbiome in beef cattle

Abstract In this study, we investigated the degree to which host genetics shape the rumen microbiome. Complex and diverse microbial communities can alter the nutrient profile available to the animal and subsequent performance. Studies of the gut microbiome have demonstrated that host genotype influences gut microbial species composition. Therefore, microbial species composition in the rumen may be a complex trait that manifests through the convergence of host-genetics and environmental factors. To test this hypothesis, we collected rumen contents and blood samples from 586 beef cattle on different diets from two locations. The rumen samples were used to sequence the V4 region of the 16S rDNA on an Illumina MiSeq platform. Animals were genotyped with various platforms and a common set of 61,974 SNP were used to conduct a genome-wide association study (GWAS) using the microbiome (OTUs, families and phyla) as response variables. The GWAS was performed using Bayesian GBLUP fitting fixed effects of cohort (location and date), and the first 2 principle components to account for population stratification. Median posterior genomic heritability estimates were 0.110, 0.124, and 0.141 at the OTU, family and phylum taxonomic level, respectively. The top 8 1-Mb windows for OTUs, families and phyla were located on 7 different chromosomes. These regions affect the rumen microbiota in multiple ways; some (chromosome 19; position 3.0–4.0 Mb) are associated with closely related taxa (Prevotellaceae, Paraprevotellaceae, and RF16), some (chromosome 27; position 3.0–4.0 Mb) are associated with distantly related taxa (Prevotellaceae, Fibrobacteraceae, RF16, RFP12, S24-7, Lentisphaerae, and Tenericutes) and others (chromosome 23; position 0.0–1.0) controlling both related and unrelated taxa. Overall, the 8 regions identified control 11 different families and 6 different phyla. This study shows that host genetics can affect rumen bacterial community members and points towards the possibility that genomics can be used to manipulate the rumen microbiome.

Comparison of flow regimes on biocorrosion of steel pipe weldments: Community composition and diversity of biofilms

Worldwide, the corrosion of petroleum pipelines is the cause of severe operational failures and damages to the environment, and the majority of them may have been intensified by microbial activities. However, few scientific publications have investigated the influence of seawater with indigenous microorganisms in internal corrosion of welded joints in long-distance pipelines, which has motivated this study. Here, a combination of culture-based and molecular microbiological methods was applied to measure the microbial abundance, diversity and composition of biofilms formed on two corroded weldments (gas tungsten arc - GTAW and shielded metal arc - SMAW) of an API 5L X65 microalloyed steel under laminar and turbulent flow regimes using seawater from Guanabara Bay (Rio de Janeiro, Brazil). Overall, turbulent flow did not reduce the biomass of sessile microorganisms on welded joints compared to laminar flow. Phylogenetic analysis revealed that the Proteobacteria, Firmicutes and Bacteroidetes were the dominant phyla in biofilms attached to GTAW and SMAW joints. At the genus level, all samples showed similar microbial composition with dominance of Desulfovibrio. However, analysis at OTU level revealed that there were specific microorganisms in each corrosive sample, even though they were affiliated to sulfate-reducers. Thus, microbial community compositions were influenced by type of weld, flow regime and biofilm age. The results of our study will be of benefit to the further studies of weld biocorrosion and biofilm ecology within pipelines.

Leveraging Fecal Bacterial Survey Data to Predict Colorectal Tumors.

Colorectal cancer (CRC) ranks second in cancer-associated mortality and third in the incidence worldwide. Most of CRC follow adenoma-carcinoma sequence, and have more than 90% chance of survival if diagnosed at early stage. But the recommended screening by colonoscopy is invasive, expensive, and poorly adhered to. Recently, several studies reported that the fecal bacteria might provide non-invasive biomarkers for CRC and precancerous tumors. Therefore, we collected and uniformly re-analyzed these published fecal 16S rDNA sequencing datasets to verify the association and identify biomarkers to classify and predict colorectal tumors by random forest method. A total of 1674 samples (330 CRC, 357 advanced adenoma, 141 adenoma, and 846 control) from 7 studies were analyzed in this study. By random effects model and fixed effects model, we observed significant differences in alpha-diversity and beta-diversity between individuals with CRC and the normal colon, but not between adenoma and the normal. We identified various bacterial genera with significant odds ratios for colorectal tumors at different stages. Through building random forest model with 10-fold cross-validation as well as new test datasets, we classified individuals with CRC, advanced adenoma, adenoma and normal colon. All approaches obtained comparable performance at entire OTU level, entire genus level, and the common genus level as measured using AUC. When combined all samples, the AUC of random forest model based on 12 common genera reached 0.846 for CRC, although the predication performed poorly for advance adenoma and adenoma.

Gut microbiota composition is associated with temperament traits in infants

BackgroundOne of the key behavioral phenotypes in infancy are different temperament traits, and certain early life temperament traits have been shown to precede later mental health problems. Differences in the gut microbiota composition (GMC) have been suggested to link with neurodevelopment. For example, toddler temperament traits have been found to associate with differences in GMC; however, studies in infants are lacking although infancy is a rapid period of neurodevelopment as well as GM development. Thus, we aimed to investigate association between infant GMC and temperament. MethodsThe study population (n = 301, 53% boys) was drawn from the FinnBrain Birth Cohort Study. Stool samples were collected from the 2.5-month-old infants and sequenced with 16S Illumina MiSeq platform. GMC taxonomic composition (at Genus and OTU level), observed sample clusters, diversity and richness were investigated in relation to the maternal reports of Infant Behavior Questionnaire -Revised (IBQ-R) at the age of 6 months. ResultsThree sample clusters (Bifidobacterium/Enterobacteriaceae, Bacteroides, V. Dispar) based on GMC were identified, of which Bifidobacterium/Enterobacteriaceae–cluster presented with higher scores on the IBQ-R main dimension regulation and its subscale duration of orienting compared to Bacteroides-cluster. The clusters associated with temperament in a sex-dependent manner. The IBQ-R main dimension surgency (positive emotionality) was associated positively both with genus Bifidobacterium and Streptococcus. Alpha diversity had a negative association with negative emotionality and fear reactivity. ConclusionThis is the first study demonstrating associations, but not causal connections, between GMC and temperament in young infants in a prospective design.

The effects of sex and APOE genotype on the gut microbiome in EFAD transgenic mice

While the gut microbiome (GM), the collective genome of bacteria in the gastrointestinal tract, is primarily studied in metabolism and immune defense, the GM may also serve as a diagnostic tool and therapeutic target in neurological disorders, including Alzheimer's disease (AD). While age is the greatest risk factor for AD, the e4allele of APOE is the greatest genetic risk factor, increasing risk up to 15‐fold compared to APOE3, the common genotype. APOE4 is associated with the accelerated accumulation of the peptide amyloid‐b(Ab), which can aggregate to form both amyloid plaques and small soluble aggregates or oligomeric Ab (oAb), the latter considered a proximal neurotoxin. Importantly, among APOE4 carriers, females have an increased AD risk, rate of cognitive loss and accumulation of Ab42 compared to males. Although the GM of individuals with AD exhibit specific microbial differences compared to healthy controls, a greater understanding of how age, APOE genotype and sex contribute to the altered GM in AD may help determine the diagnostic potential of the GM composition. To study the interactions among these AD risk factors, we developed the EFAD‐transgenic mice, which express the human APOE genotypes and over‐express human Ab42. Thus, our hypothesis is that APOE genotype and sex interact to modulate the GM composition in EFAD mice. Fecal samples from 4 month (M) ♂ and ♀ E3FAD and E4FAD mice were sequenced and compared. The Shannon H index, a measure of species richness and diversity, identified a negative correlation between diversity and severity of AD pathology in the 4M EFAD cohorts of mice: ♂E4FAD &gt; ♀E4FAD and ♀E3FAD &gt; ♀E4FAD. Analysis of similarities (ANOSIM) demonstrated significant differences in the GM in E3FAD vs E4FAD across different taxonomic levels (operational taxonomic unit/OTU, Genus, and Family). Comparison across sex within APOE genotype revealed a significant difference between ♂E3FAD vs ♂E4FAD and ♀E3FAD vs ♀E4FAD at all taxonomic levels. Additionally, there is a significant effect for ♂E4FAD vs ♀E4FAD, though only at the OTU level. Further, heatmap analysis demonstrates clustering of ♀E4FAD samples based on 29 OTUs. Therefore, the synergistic effect of APOE4 and female sex on AD risk is exhibited by the GM, observed by the stratification of the EFAD cohorts. This study is the first step in defining the composition of the GM as a function APOE genotype and sex modulation of AD pathology.Support or Funding InformationLaDu lab funding includes institutional funds from the University of Illinois College of Medicine, the Bridge to the Doctorate Fellowship, and the Honor's College Undergraduate Research Award at the University of Illinois at Chicago.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Diverse Environmental Microbiota as a Tool to Augment Biodiversity in Urban Landscaping Materials.

Human activities typically lead to simplified urban diversity, which in turn reduces microbial exposure and increases the risk to urban dwellers from non-communicable diseases. To overcome this, we developed a microbial inoculant from forest and agricultural materials that resembles microbiota in organic soils. Three different sand materials (sieved, safety, and sandbox) commonly used in playgrounds and other public spaces were enriched with 5% of the inoculant. Skin microbiota on fingers (identified from bacterial 16S rDNA determined using Illumina MiSeq sequencing) was compared after touching non-enriched and microbial inoculant-enriched sands. Exposure to the non-enriched materials changed the skin bacterial community composition in distinct ways. When the inoculant was added to the materials, the overall shift in community composition was larger and the differences between different sand materials almost disappeared. Inoculant-enriched sand materials increased bacterial diversity and richness but did not affect evenness at the OTU level on skin. The Firmicutes/Bacteroidetes ratio was higher after touching inoculant-enriched compared to non-enriched sand materials. The relative abundance of opportunistic pathogens on skin was 40–50% before touching sand materials, but dropped to 14 and 4% after touching standard and inoculant-enriched sand materials, respectively. When individual genera were analyzed, Pseudomonas sp. and Sphingomonas sp. were more abundant after touching standard, non-enriched sand materials, while only the relative abundance of Chryseobacterium sp. increased after touching the inoculant-enriched materials. As Chryseobacterium is harmless for healthy persons, and as standard landscaping materials and normal skin contain genera that include severe pathogens, the inoculant-enriched materials can be considered safe. Microbial inoculants could be specifically created to increase the proportion of non-pathogenic bacterial taxa and minimize the transfer of pathogenic taxa. We recommend further study into the usability of inoculant-enriched materials and their effects on the bacterial community composition of human skin and on the immune response.

Gut microbiota of the European Brown Hare (Lepus europaeus)

Diseases of the gastrointestinal tract due to changes in the bacterial flora have been described with increasing incidence in the European brown hare. Despite extensive demographic and phylogeographic research, little is known about the composition of its gut microbiota and how it might vary based on potential environmental or host factors. We analysed the intestinal and faecal microbiota of 3 hare populations by Illumina MiSeq 16S rRNA gene amplicon sequencing. The phyla and OTU abundance composition differed significantly between intestinal and faecal samples (PERMANOVA: P = 0.002 and P = 0.031, respectively), but in both sample types Firmicutes and Bacteroidetes dominated the microbial community composition (45.51% and 19.30% relative abundance). Intestinal samples contained an enrichment of Proteobacteria compared with faecal samples (15.71-fold change, P < 0.001). At OTU level, a significant enrichment with best BLAST hits to the Escherichia-Shigella group, Eubacterium limosum, Sphingomonas kyeonggiensis, Flintibacter butyricus and Blautia faecis were detected in intestinal samples (P < 0.05). In our statistical model, geographic location and possibly associated environmental factors had a greater impact on the microbiota composition than host factors. Population had a significant effect on the composition of abundant intestinal and faecal OTUs, and on the abundance of potential pathogenic bacteria of the family Enterobacteriaceae, regularly associated with intestinal dysbiosis in hares, in faecal samples. Our study is the first to describe the microbiota in brown hares and provides a foundation to generate hypothesis aiming to test the role of gut health in population fluctuations of the species.

Mucin degradation niche as a driver of microbiome composition and Akkermansia muciniphila abundance in a dynamic gut model is donor independent

Akkermansia muciniphila, an abundant mucin degrading intestinal bacterium, has been correlated with human health in various studies. The in vitro SHIME model was used to reach a mechanistic understanding of A. muciniphila's colonization preferences and its response to environmental parameters such as colon pH and mucins. These insight can help to identify the optimal conditions for successful in vivo application. After a period of mucin deprivation, we found that mucin supplementation resulted in significantly different microbial communities, with more Akkermansia, Bacteroides and Ruminococcus. Mucin treatment accounted for 26% of the observed variation in the microbial community at OTU level (P = 0.001), whereas the donor effect was limited (8%) (P = 0.035), indicating mucins to constitute an important ecological niche shaping the microbiota composition. The effect of colonic pH had a less profound impact on the microbiome with both pH and donor origin explaining around 10% of the variability in the dataset. Yet, higher simulated colonic pH had a positive impact on Akkermansia abundance while short chain fatty acid analysis displayed a preference for propionate production with higher colonic pH. Our results show that mucins as nutritional resource are a more important modulator of the gut microbiome than colon pH as environmental factor.

Application of MootralTM Reduces Methane Production by Altering the Archaea Community in the Rumen Simulation Technique.

The reduction of methane emissions by ruminants is a highly desirable goal to mitigate greenhouse gas emissions. Various feed additives have already been tested for their ability to decrease methane production; however, practical use is often limited due to negative effects on rumen fermentation or high costs. Organosulphur compounds from garlic (Allium sativum) and flavonoids have been identified as promising plant-derived compounds which are able to reduce methane production. Here, we evaluated the effects of a combination of garlic powder and bitter orange (Citrus aurantium) extracts, Mootral, on ruminal methane production, ruminal fermentation and the community of methanogenic Archaea by using the rumen simulation technique as ex vivo model. The experiment consisted of an equilibration period of 7 days, an experimental period of 8 days and a withdrawal period of 4 days. During the experimental period three fermenters each were either treated as controls (CON), received a low dose of Mootral (LD), a high dose of Mootral (HD), or monensin (MON) as positive control. Application of Mootral strongly reduced the proportion of methane in the fermentation gas and the production rate of methane. Moreover, the experimental mixture induced a dose-dependent increase in the production rate of short chain fatty acids and in the molar proportion of butyrate. Some effects persisted during the withdrawal period. Both, single strand conformation polymorphism and Illumina MiSeq 16S rRNA amplicon sequencing indicated an archaeal community distinct from CON and MON samples in the LD and HD samples. Among archaeal families the percentage of Methanobacteriaceae was reduced during application of both doses of Mootral. Moreover, several significant differences were observed on OTU level among treatment groups and after withdrawal of the additives for LD and HD group. At day 14, 4 OTUs were positively correlated with methane production. In conclusion this mixture of garlic and citrus compounds appears to effectively reduce methane production by alteration of the archaeal community without exhibiting negative side effects on rumen fermentation.

Consistent patterns of high alpha and low beta diversity in tropical parasitic and free-living protists.

Tropical animals and plants are known to have high alpha diversity within forests, but low beta diversity between forests. By contrast, it is unknown whether microbes inhabiting the same ecosystems exhibit similar biogeographic patterns. To evaluate the biogeographies of tropical protists, we used metabarcoding data of species sampled in the soils of three lowland Neotropical rainforests. Taxa-area and distance-decay relationships for three of the dominant protist taxa and their subtaxa were estimated at both the OTU and phylogenetic levels, with presence-absence and abundance-based measures. These estimates were compared to null models. High local alpha and low regional beta diversity patterns were consistently found for both the parasitic Apicomplexa and the largely free-living Cercozoa and Ciliophora. Similar to animals and plants, the protists showed spatial structures between forests at the OTU and phylogenetic levels, and only at the phylogenetic level within forests. These results suggest that the biogeographies of macro- and micro-organismal eukaryotes in lowland Neotropical rainforests are partially structured by the same general processes. However, and unlike the animals and plants, the protist OTUs did not exhibit spatial structures within forests, which hinders our ability to estimate the local and regional diversity of protists in tropical forests.

Synchrony of Eukaryotic and Prokaryotic Planktonic Communities in Three Seasonally Sampled Austrian Lakes.

Freshwater systems are characterized by an enormous diversity of eukaryotic protists and prokaryotic taxa. The community structures in different lakes are thereby influenced by factors such as habitat size, lake chemistry, biotic interactions, and seasonality. In our study, we used high throughput 454 sequencing to study the diversity and temporal changes of prokaryotic and eukaryotic planktonic communities in three Austrian lakes during the ice-free season. In the following year, one lake was sampled again with a reduced set of sampling dates to observe reoccurring patterns. Cluster analyses (based on SSU V9 (eukaryotic) and V4 (prokaryotic) OTU composition) grouped samples according to their origin followed by separation into seasonal clusters, indicating that each lake has a unique signature based on OTU composition. These results suggest a strong habitat-specificity of microbial communities and in particular of community patterns at the OTU level. A comparison of the prokaryotic and eukaryotic datasets via co-inertia analysis (CIA) showed a consistent clustering of prokaryotic and eukaryotic samples, probably reacting to the same environmental forces (e.g., pH, conductivity). In addition, the shifts in eukaryotic and bacterioplanktonic communities generally occurred at the same time and on the same scale. Regression analyses revealed a linear relationship between an increase in Bray–Curtis dissimilarities and elapsed time. Our study shows a pronounced coupling between bacteria and eukaryotes in seasonal samplings of the three analyzed lakes. However, our temporal resolution (biweekly sampling) and data on abiotic factors were insufficient to determine if this was caused by direct biotic interactions or by reacting to the same seasonally changing environmental forces.

Different Height Forms of Spartina alterniflora Might Select Their Own Rhizospheric Bacterial Communities in Southern Coast of China.

In the southernmost part of coast of China, two height forms of Spartina alterniflora, tall and short, have invaded Leizhou Peninsula within the last decade. However, the effect of different height forms of Spartina alterniflora on plant-microbe interaction has not been clarified. Here, the community structures of rhizosphere bacteria and the abundance of N- and S-cycling functional genes associated with selected S. alterniflora were investigated in the field and a common garden. The community structure of tall-form S. alterniflora was distinct from short-form S. alterniflora at OTU level in the field, even after transplantation into a common garden. The abundance of bacterial amoA, nirS, and nosZ in tall S. alterniflora was significantly greater than those in short S. alterniflora in the field; however, this difference disappeared in a 1-year common garden experiment. These results suggested that compared with the tall-form S. alterniflora, the rhizosphere of short-form S. alterniflora harbored fewer nitrification-denitrification related microorganisms, which might benefit from conserving N in an N limited habitat. Together, our results suggested that tall- and short-form S. alterniflora can host their specific rhizosphere microbial communities and had different strategies of N usage via selecting the composition of rhizosphere bacterial assemblages, which in turn might determine the growth and invasiveness of S. alterniflora in its introduced range.

Microbial communities in soil profile are more responsive to legacy effects of wheat-cover crop rotations than tillage systems

Declining trends in soil health under continuous monoculture systems of winter wheat are a concern for sustainable production in the Southern Great Plains of the US. This study was conducted to evaluate the long-term implementation of conservation tillage in combination with nitrogen treatments and summer cover crop (cowpeas) rotations with winter wheat, for their legacy effects on soil health attributes of microbial communities and soil organic carbon (SOC). Microbial biomass and composition were estimated, along with soil physico-chemical parameters in the soil profile during the annual rotation cycle of wheat and cover crops. Positive legacy effects of cover crop rotations were evident, as arbuscular mycorrhizal fungi (AMF) biomass during the wheat-growing season was significantly higher in cover crop treatments (by around 30-70%) compared to summer fallow treatment. Some dominant taxons such as Acidobacteria, Actinobacteria, Proteobacteria (>70% of prokaryotic relative abundance) and Ascomycota (>50% of fungal relative abundance) were detected in all experimental treatments. Microbial composition did not significantly change at phylum level, although some reorganization at OTU level was evident throughout the soil profile, mostly because of nitrogen treatments. Several Glomeromycota OTUs were significantly altered by soil depth and by nitrogen fertilization suggest distinct mycorhizosphere interactions in subsurface soil than the surface soil. Tillage treatment did not significantly alter the microbial abundance and their diversity. Differences in microbial biomass-C concentration among experimental treatments did not result in a change in SOC concentrations within the soil profile. Results of this study demonstrated that summer cowpea appeared to be an effective cover crop for enhancing beneficial microbial biomass and expansion of the mycorrhizosphere to deeper soil layers. Cover crop rotations appeared to be a suitable option for rapidly enhancing soil health in winter wheat production systems.