Wiraswati SM, Wahyudi AT, Rusmana I, Nawangsih AA. 2018. TRFLP analysis for revealing the diversity of rice phyllosphere bacteria. Biodiversitas 19: 1743-1749. Phyllosphere environment of rice plant ...is usually inhabited by diverse bacteria which mostly contribute beneficial effects to the plant fitness. TRFLP method is a rapid and straightforward method to determine the bacterial diversity of many environments, including rice phyllosphere environment. This study aimed to analyze rice phyllosphere bacterial diversity of healthy rice plant cultivar Ciherang obtained from Sukabumi, Jasinga, and Situgede. The bacterial genomes were amplified and digested with two restriction enzymes, i.e., MspI and BstUI. The bacterial diversity (H’ index) and evenness (E index) were calculated from the peak value. From TRFs analysis, Betaproteobacteria and Pseudomonadales were dominantly found in nearly all samples with different relative abundance. In addition, Alphaproteobacteria and Gammaproteobacteria were also dominant in the several samples. The unique bacteria groups were inhabited in the sample from specific regions with certain growth phase. This finding informs us that the geographical factors might be more influent than the growth phase factor. Furthermore, the bacterial diversity and evenness of the metagenomic approach are higher than cultivation-dependent approach.
Background and aims To assess the impacts of soil microbes and plant genotype on the composition of maize associated bacterial communities. Methods Two genotypes of Brazilian maize were planted ...indoors on sterile sand, a deep underground subsoil, and a nutrient-rich topsoil from the Amazon jungle (terra preta). DNA was extracted from rhizospheres, phyllospheres, and surface sterilized roots for 16S rDNA fingerprinting and next generation sequencing. Results Neither plant genotype nor soil type appeared to influence bacterial diversity in phyllospheres or endospheres. Rhizospheres showed strikingly similar 16S rDNA ordination of both fingerprinting and sequencing data, with soil type driving grouping patterns and genotype having a significant impact only on sterile sand. Rhizospheres grown in non-sterile soils contained greater bacterial diversity than sterile-sand grown ones, however the dominant OTUs (species of Proteobacteria and Bacteroidetes) were found in all rhizospheres suggesting seeds as a common source of inoculum. Rhizospheres of the commercial hybrid appeared to contain less bacterial diversity than the landrace. Conclusions Maize rhizospheres receive diverse bacteria from soil, are influenced by the genotype or treatment of the seed, and are dominated by species of Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. As many dominant 16S rDNA sequences were observed in rhizospheres grown in both sterile and non-sterile substrate, we conclude that the most common bacterial cells in juvenile maize rhizospheres are seed transmitted.
•Cacao agroforestry systems alter the soil biomass of specific microbial groups.•Cover crops alter soil microbial community structure in cacao production systems.•Soil pH gradients influence ...community structure more than management system.
Cacao (Theobroma cacao) trees are grown in tropical regions worldwide for chocolate production. We studied the effects of agroforestry management systems and cover cropping on soil microbial communities under cacao in two different replicated field experiments in Peru. In the first experiment, two agroforestry systems, Improved Traditional Agroforestry System (ITAS) and Improved Natural Agroforestry System (INAS), were compared. ITAS was a ‘slash and burn’ system in which all native vegetation was removed prior to replanting with cacao and other trees while INAS used selective removal of uneconomical trees followed by cacao planting. Soil microbial communities were analyzed by phospholipid fatty acid (PLFA) analysis and terminal restriction fragment length polymorphism (TRFLP) analysis. Soils in the ITAS system had altered microbial community structure and a lower Gram-negative to Gram-positive ratio when compared to soils in the INAS system. However, soil microbial community structure was also affected by a large soil pH gradient (three pH units) across this experiment. In the cover crop experiment, five cover crops, Arachis pintoi (perennial peanut), Calopogonium mucunoides (calopo), Canavalia ensiformis (jackbean), Centrosema macrocarpum (centro), and Callisia repens (callisia), and two controls (one with and one without nitrogen fertilization), were compared. Cover cropping with centro or perennial peanut increased the Gram-negative to Gram-positive ratio, while centro reduced the fungal biomass. Microbial community structure was significantly affected by cover cropping. Our results indicate that management systems and cover cropping can affect soil microbial community structure in tropical agroforestry systems, but the effects of soil edaphic properties must be considered as well.
•Marker microbiome clusters are determined by operational parameters.•A weighting of operations parameters was derived from higher to lower importance.•Biotic interactions between specific community ...arrangements were revealed.•Each anaerobic digestion plant develops its own unique microbiome.•Specialists are potentially hidden drivers under process-inconvenient conditions.
In this study, microbiomes of 36 full-scale anaerobic digesters originated from 22 different biogas plants were compared by terminal restriction fragment length polymorphism (TRFLP) analysis.
Regarding the differences in microbial community composition, a weighting of the environmental parameters could be derived from higher to lower importance as follows: (i) temperature, (ii) TAN and NH3 concentrations and conductivity, and (iii) the chemical composition of the supplied feedstocks.
Biotic interactions between specific bacterial and archaeal community arrangements were revealed, whereby members of the phyla Bacteroidetes and Cloacimonetes combined with the archaeal genus Methanothrix dominated the conversion of homogeneous feedstocks, such as waste water sludge or industrial waste.
As most of the detected TRFs were only found in a certain number of anaerobic digestion plants, each plant develops its unique microbiome. The putative rare species, the specialists, are potentially hidden drivers of microbiome functioning as they provide necessary traits under, e.g., process-inconvenient conditions.
Tomato vine decline (TVD) disease complex results in fruit yield loss, but what soil management strategies might mitigate it? In commercial fields with a history of TVD, five approaches (soil organic ...amendments and transplant treatments) were evaluated for their impact on fruit yield, fruit quality, and microbial abundance or diversity at four site-years. One site-year had very high TVD pressure and high variability with no yield differences, thus efforts focused on the remaining site-years. Marketable yield was not different among treatments but numerically followed a trend similar to total yield. Amending soil with poultry manure delayed maturity (i.e., increased proportion of green fruit) and had the greatest total yield increases of 17.2%, congruent with decreased abundance of root pathogens (Verticillium dahliae, Rhizopicnis vagum). Microbial DNA fingerprinting data of rhizospheres, roots and (or) stems suggested treatments did not significantly shift the total diversity fungal nor bacterial populations, but the aforementioned pathogen loads were reduced with the application of organic amendments relative to the untreated control. While drenching tomato transplants with pseudomonad culture increased their presence in roots, pathogen load was not reduced relative to the untreated control. Overall, these results show that soil organic amendments were able to improve tomato total yield in two of four site-years without reducing fruit quality (i.e., soluble solids, pH, colour), perhaps, in part, due to their ability to suppress specific root pathogens in commercial fields.
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•First investigation of microbial stratification in full-scale anaerobic digestion plants.•No indications for significant zoning of microbial communities found.•Stirring and feeding ...regimes were sufficient to homogenize the microorganisms.
In anaerobic digestion plants (ADs), homogenization of the feed, fermenter content and microbial communities is crucial for efficient and robust biogas production. However, mixing also requires a significant amount of energy. For an 850 m3 agricultural AD equipped with eight sampling ports, we investigated whether different feeding and stirring regimes enable a sufficient homogenization of the microbial community using metaproteomics and terminal restriction fragment length polymorphism (TRFLP) analysis. Systematic comparison of samples taken at the top and the bottom as well as at the rim and the center of the AD using scatter plots and students t-test revealed only a small number of differences in metaproteins, taxonomies and biological processes. Obviously, the applied stirring and feeding conditions were sufficient to largely homogenize the content of the AD.
Colonial nesting and roosting birds can degrade their habitat by soil salinization, eutrophication, and acidification associated with excessive deposition of avian excreta. We studied the impact of a ...protected wading bird colony on soil microbial communities from cork oak woodlands in Doñana National Park (SW Spain). Over one year we analyzed soil properties (pH, salinity, soluble N and P forms, extractable organic carbon - EOC -), microbial activity (basal respiration, community-level physiological profile, extracellular enzyme activities) and community structure (fungal, bacterial and archaeal terminal restriction fragments -TRFs-) along a gradient of bird nesting intensity. Bird nesting largely impacted soil chemical environment, with increases from 25 to 500 μS cm−1 in soil salinity, from 6 to 725 mg kg−1 in soil P, from 5 to 22 mg kg−1 in N-NH4, and from 5.4 to 245 mg kg−1 in N-NO3 between the extremes of the nesting intensity gradient in the wet season. Most of these chemical changes were enhanced in the dry season. We observed positive linear or log-linear relationships between the bird nesting footprint on soils (indicated by an integrated soil chemistry index) and microbial biomass, basal respiration and most of the studied enzyme activities. This was likely due to the concurrent increases in EOC along the avian intensity gradient, which counteracted the negative impacts of salinity. Soil P and EOC were the main drivers for fungal, bacterial and archaeal TRFs diversity. Bacterial TRFs richness and diversity index decreased along the avian intensity gradient in the dry season, while archaeal TRFs diversity increased in those soils highly salinized by excess of avian excreta deposition. Our study clearly shows that this oversized bird colony has profound effects on soil chemistry and biological activity, and highlights the need for a re-evaluation of management strategies in this protected area, towards a greater consideration of soil processes in conservation priorities.
•The impact of a protected bird colony on soil microbial communities was studied.•Birds largely impacted soil chemistry and microbial community structure and function.•Bacterial diversity decreased with avian intensity, and archaeal diversity increased.•Nesting birds compromised the maintenance of the native soil microbial communities.
Soil fungi are highly diverse and act as the primary agents of nutrient cycling in forests. These fungal communities are often dominated by mycorrhizal fungi that form mutually beneficial ...relationships with plant roots and some mycorrhizal fungi produce extracellular and cell-bound enzymes that catalyze the hydrolysis of nitrogen (N)- and phosphorus (P)- containing compounds in soil organic matter. Here we investigated whether the community structure of different types of mycorrhizal fungi (arbuscular and ectomycorrhizal fungi) is correlated with soil chemistry and enzyme activity in a northern hardwood forest and whether these correlations change over the growing season. We quantified these relationships in an experimental paired plot study where white-tailed deer (access or excluded 4.5 yrs) treatment was crossed with garlic mustard (presence or removal 1 yr). We collected soil samples early and late in the growing season and analyzed them for soil chemistry, extracellular enzyme activity and molecular analysis of both arbuscular mycorrhizal (AM) and ectomycorrhizal/saprotrophic fungal communities using terminal restriction fragment length polymorphism (TRFLP). AM fungal communities did not change seasonally but were positively correlated with the activities of urease and leucine aminopeptidase (LAP), enzymes involved in N cycling. The density of garlic mustard was correlated with the presence of specific AM fungal species, while deer exclusion or access had no effect on either fungal community after 4.5 yrs. Ectomycorrhizal/saprotrophic fungal communities changed seasonally and were positively correlated with most soil enzymes, including enzymes involved in carbon (C), N and P cycling, but only during late summer sampling. Our results suggest that fine scale temporal and spatial changes in soil fungal communities may affect soil nutrient and carbon cycling. Although AM fungi are not generally considered capable of producing extracellular enzymes, the correlation between some AM taxa and the activity of N acquisition enzymes suggests that these fungi may play a role in forest understory N cycling.
► AM fungi were stable over time and correlated with urease and LAP activity. ► ECM/saprotrophic fungi changed between early and late summer sampling. ► ECM/saprotrophic fungi were positively correlated with most soil enzymes. ► Excluding deer for 4 years did not affect soil fungi. ► AM fungi were significantly correlated with the density of garlic mustard adults.
Specific interactions between parasite genotypes and host genotypes (Gₚ × Gₕ) are commonly found in invertebrate systems, but are largely lacking a mechanistic explanation. The genotype of ...invertebrate hosts can be complemented by the genomes of microorganisms living on or within the host (‘microbiota’). We investigated whether the bacterial gut microbiota of bumble bees (Bombus terrestris) can account for the specificity of interactions between individuals from different colonies (previously taken as host genotype proxy) and genotypes of the parasite Crithidia bombi. For this, we transplanted the microbiota between individuals of six colonies. Both the general infection load and the specific success of different C. bombi genotypes were mostly driven by the microbiota, rather than by worker genotype. Variation in gut microbiota can therefore be responsible for specific immune phenotypes and the evolution of gut parasites may be driven by interactions with ‘microbiota types’ as well as with host genotypes.
This study investigated the environmental health risks to soil and potential risks to groundwater associated with long term (8–18years) greywater disposal practices. Land application of greywater is ...likely to have environmental impacts, which may be positive or negative. Greywater can contain plant macronutrients that may benefit plant growth. Conversely, high levels of surfactants, oils, grease, sodium and potentially pathogenic organisms may negatively impact environmental and human health. In this study, land disposal of untreated greywater was practiced at five coastal domestic properties. At each property, soil samples were collected at two depths from areas used for greywater disposal and from control areas that were not exposed to greywater. Soils were analysed for chemical and biological responses to greywater exposure. Generally, greywater irrigated soils had higher pH, Olsen P, base saturation, and increased soil microbial activity (as measured by biomass carbon, basal respiration and dehydrogenase activity). A pH of >9 was recorded for some greywater treated soil samples. Escherichia coli (E. coli) were detected at up to 103MPN/g in the greywater exposed surface soils at some sites. Terminal Restriction Fragment Length Polymorphism (TRFLP) analysis revealed that greywater affected the soil microbial community structure, which may have implications for soil health and fertility. Overall, this study shows that the long-term application of greywater at the investigated sites had a moderate impact on the soil environment. This may have been due to the sandy soils and high rainfall that would flush the soil. Increases in microbial biomass and dehydrogenase indicate that greywater application may be beneficial for plant growth. However, high levels of E. coli in some soils may be a risk to human health and sub-surface irrigation should be the recommended application method.
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•Long term greywater disposal impacted the soil environment.•Results included increased pH, SAR, EC and dehydrogenase activity.•The soil microbial community was affected by greywater disposal.
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