Distribution Of Phyla Research Articles

Structure, variation, and assembly of the root-associated microbiomes of rice

Plants depend upon beneficial interactions between roots and microbes for nutrient availability, growth promotion, and disease suppression. High-throughput sequencing approaches have provided recent insights into root microbiomes, but our current understanding is still limited relative to animal microbiomes. Here we present a detailed characterization of the root-associated microbiomes of the crop plant rice by deep sequencing, using plants grown under controlled conditions as well as field cultivation at multiple sites. The spatial resolution of the study distinguished three root-associated compartments, the endosphere (root interior), rhizoplane (root surface), and rhizosphere (soil close to the root surface), each of which was found to harbor a distinct microbiome. Under controlled greenhouse conditions, microbiome composition varied with soil source and genotype. In field conditions, geographical location and cultivation practice, namely organic vs. conventional, were factors contributing to microbiome variation. Rice cultivation is a major source of global methane emissions, and methanogenic archaea could be detected in all spatial compartments of field-grown rice. The depth and scale of this study were used to build coabundance networks that revealed potential microbial consortia, some of which were involved in methane cycling. Dynamic changes observed during microbiome acquisition, as well as steady-state compositions of spatial compartments, support a multistep model for root microbiome assembly from soil wherein the rhizoplane plays a selective gating role. Similarities in the distribution of phyla in the root microbiomes of rice and other plants suggest that conclusions derived from this study might be generally applicable to land plants.

Predominant bacterial and fungal assemblages in agricultural soils during a record drought/heat wave and linkages to enzyme activities of biogeochemical cycling

Identification of microbial assemblages predominant under natural extreme climatic events will aid in our understanding of the resilience and resistance of microbial communities to climate change. From November 2010 to August 2011, the Southern High Plains (SHP) of Texas, USA, received only 39.6mm of precipitation (vs. the historical average of 373mm) and experienced the three hottest months (June–August 2011) since record keeping began in 1911. The objective of this study was to characterize soil bacterial (16 S rRNA gene) and fungal (internal transcribed spacer 1–4, ITS1-ITS4) species distribution and diversity via pyrosequencing during the peak of the drought/heat wave in July 2011 and when the Drought Index and temperatures were lower in March 2012. Samples were collected from two different soil types (loam and sandy loam) under two different dryland cropping histories (monoculture vs. rotation). Fungal Diversity Indexes were significantly higher after the drought/heat wave while Bacterial Indexes were similar. Bacterial phyla distribution in July 2011 was characterized by lower relative abundance of Acidobacteriaand Verrucomicrobia, and greater relative abundance of Proteobacteria, Chloroflexi, Actinobacteria and Nitrospirae than March 2012 samples. Further grouping of pyrosequencing data revealed approximately equal relative proportions of Gram positive (G+) and Gram negative (G−) bacteria in July 2011, while G− bacteria predominated in March 2012. Fungal class Dothideomycetes was approximately two times greater in July 2011 than in March 2012, while the class Sordariomycetes and a group of unidentified OTUs from Ascomycota increased from July 2011 to March 2012. Microbial community composition was less influenced by management history than by the difference in climatic conditions between the sampling times. Correspondence analysis identified assemblages of fungal and bacterial taxa associated with greater enzyme activities (EAs) of C, N, or P cycling found during the drought/heat wave. Microbial assemblages associated with arylsulfatase activity (key to S cycling), which increased after the drought/heat wave, were identified (Streptomyces parvisporogenes, Terrimonas ferruginea and Syntrophobacter sp.) regardless of the soil and management history. The distinct microbial composition found in July 2011 may represent assemblages essential to maintaining ecosystem function during extreme drought and intense heat waves in semiarid agroecosystems.

Lung microbiota and bacterial abundance in patients with bronchiectasis when clinically stable and during exacerbation.

Characterization of bacterial populations in infectious respiratory diseases will provide improved understanding of the relationship between the lung microbiota, disease pathogenesis, and treatment outcomes. To comprehensively define lung microbiota composition during stable disease and exacerbation in patients with bronchiectasis. Sputum was collected from patients when clinically stable and before and after completion of antibiotic treatment of exacerbations. Bacterial abundance and community composition were analyzed using anaerobic culture and 16S rDNA pyrosequencing. In clinically stable patients, aerobic and anaerobic bacteria were detected in 40 of 40 (100%) and 33 of 40 (83%) sputum samples, respectively. The dominant organisms cultured were Pseudomonas aeruginosa (n = 10 patients), Haemophilus influenzae (n = 12), Prevotella (n = 18), and Veillonella (n = 13). Pyrosequencing generated more than 150,000 sequences, representing 113 distinct microbial taxa; the majority of observed community richness resulted from taxa present in low abundance with similar patterns of phyla distribution in clinically stable patients and patients at the onset of exacerbation. After treatment of exacerbation, there was no change in total (P = 0.925), aerobic (P = 0.917), or anaerobic (P = 0.683) load and only a limited shift in community composition. Agreement for detection of bacteria by culture and pyrosequencing was good for aerobic bacteria such as P. aeruginosa (κ = 0.84) but poorer for other genera including anaerobes. Lack of agreement was largely due to bacteria being detected by pyrosequencing but not by culture. A complex microbiota is present in the lungs of patients with bronchiectasis and remains stable through treatment of exacerbations, suggesting that changes in microbiota composition do not account for exacerbations.

Microbial Community Composition as Affected by Dryland Cropping Systems and Tillage in a Semiarid Sandy Soil

This study evaluated microbial communities of soil (0–10 cm) as affected by dryland cropping systems under different tillage practices after 5 years. The soil type was an Olton sandy loam with an average of 16.4% clay, 67.6% sand and 0.65 g kg−1 of organic matter (OM). The cropping systems evaluated were grain sorghum (Sorghum bicolor L.)—cotton (Gossypium hirsutum) (Srg-Ct), cotton-winter rye (Secale cereale)-grain sorghum (Ct-Rye-Srg), and a rotation of forage (f) sorghum (Sorghum bicolor L. and Sorghum sudanense) with winter rye (Srf-Rye), which were under no-tillage (nt) and conventional tillage (ct) practices. Soil microbial communities under cotton based cropping systems (Srg-Ct and Ct-Rye-Srg) showed lower fungal:bacterial ratios compared to the soil under Srf-Rye. Soil under Srf-Rye showed higher population densities of Bacteroidetes and Proteobacteria while lower Actinobacteria compared to Srg-Ct and Ct-Rye-Srg. Chloroflexi, Gemmatimonadetes and Verrucomicrobiae were higher in tilled soil compared to the no-tilled plots. Regardless the limited irrigation available to sustain agricultural production within these dryland cropping systems, this study demonstrated that differences in microbial communities are more affected by crop rotation than tillage management history. Although soil fungal diversity was not analyzed in this study, pyrosequencing suggests that tillage practices can affect bacterial phyla distribution in this sandy soil.

Pyrosequencing analysis for characterization of soil bacterial populations as affected by an integrated livestock-cotton production system

Bacterial tag-encoded FLX amplicon pyrosequencing of the 16S rDNA gene was used to evaluate bacterial diversity of a clay loam soil (fine, mixed, thermic Torrertic Paleustolls) after 10 years under an integrated livestock (beef)-cotton ( Gossypium hirsutum L.) production system compared to continuous cotton in a semiarid region. In the integrated system, cattle alternatively grazed a perennial warm-season grass [ Bothriochloa bladhii (Retz) S.T. Blake] paddock and small grains grown in two paddocks of a wheat ( Triticum aestivum L.)-fallow-rye ( Secale cereal L.)-cotton rotation. Areas excluded from grazing in the integrated system were also evaluated. Maximum observed number of unique sequences operational taxonomic units (OTU) at 3% dissimilarity level (roughly corresponding to the species level) corresponded to 1200 and 1100 at 0–5 and 5–15 cm depths, respectively. Predominant phyla (up to 65% of abundance) at 0–5 and 5–15 cm in this soil were Proteobacteria, Actinobacteria and Gemmatimonadetes. Proteobacteria were predominant in soil under all components of the integrated livestock-cotton system compared to continuous cotton whereas Bacteroidetes were predominant under continuous cotton. Firmicutes (i.e., Clostridia) and Chlorofexi (i.e., Thermomicrobia) were more abundant in soil under fallow periods of the rotation compared to under cotton (Rye- Cotton-Wheat-Fallow or continuous cotton) or grass (i.e., pasture). The lowest OTUs were detected in soil under fallow periods of the rotation (Wheat- Fallow-Rye-Cotton) compared to the other treatments. Grazing effects were significant for Actinobacteria, Proteobacteria and Chlorofexi. Compared to the continuous cotton system, this study revealed significant changes in bacterial phyla distribution under integrated livestock-cotton systems for a semiarid soil after 10 years. Positive correlations were found between certain bacteria ( Proteobacteria, Firmicutes, Chloroflexi, Verrucomicrobiae and Fibrobacteres) and the activities of alkaline phosphatase and β-glucosidase or β-glucosaminidase.