Contribution Of Abiotic Factors Research Articles

Toward a holistic view of orchard ecosystem dynamics: A comprehensive review of the multiple factors governing development or suppression of apple replant disease.

Replant diseases are a common occurrence in perennial cropping systems. In apple, progress toward the development of a universally effective disease management strategy, beyond the use of broad-spectrum soil fumigants, is impeded by inconsistencies in defining replant disease etiology. A preponderance of evidence attributes apple replant disease to plant-induced changes in the soil microbiome including the proliferation of soilborne plant pathogens. Findings from alternative studies suggest that the contribution of abiotic factors, such as the accumulation of phenolic detritus from previous orchard plantings, may play a part as well. Engineering of the resident soil microbiome using resource-based strategies is demonstrating potential to limit activity of replant pathogens and improve productivity in newly established orchards. An understanding of factors promoting the assembly of a disease-suppressive soil microbiome along with consideration of host factors that confer disease tolerance or resistance is imperative to the developing a more holistic view of orchard ecosystem dynamics. Here, we review the literature concerning the transition of orchard soil from a healthy state to a replant disease-conducive state. Included in the scope of this review are studies on the influence of soil type and geography on the apple replant pathogen complex. Furthermore, several tolerance and innate resistance mechanisms that have been described in apple to date, including the role of root chemistry/exudates are discussed. Finally, the interplay between apple rootstock genotype and key resource-based strategies which have been shown to “reshape” the plant holobiont in favor of a more prophylactic or disease-suppressive state is highlighted.

Depth effects on bacterial community assembly processes in paddy soils

Bacterial communities in soil play a key role in carbon (C) and nutrient cycling. Unravelling how bacterial community assemble and distribute with soil depth is a prerequisite for understanding microbial functions, nutrient cycling and management. Twenty-six rice fields in a typical red soil area in a wet subtropical climate were sampled in the topsoil (0–10 and 10–20 cm) and subsoil (20–40 cm). Physico-chemical soil properties, quantitative fluorescence PCR and high-throughput sequencing were used to analyse the V4 region of 16S rDNA. The rRNA operon copy number and alpha diversity decreased continuously with soil depth because of reduced access to carbon, energy, oxygen and nutrients. The relative abundance of the dominant phyla Proteobacteria and Actinobacteria decreased with increasing soil depth, whereas the opposite trend was observed for the phylum Nitrospirae. The interaction intensity between taxa increased with depth, as limited carbon and nutrients in the undisturbed subsoil lead to the cooccurrence of taxa with similar ecological niches that cooperated to reduce functional redundancy. The higher modularity of the bacterial network in the topsoil is associated with greater environmental perturbations (flooding, fertilization, etc.) to maintain the robustness of the microbial community. Bacterial community assembly processes were stochastic up to 40 cm, but ecological drift was the predominant process in the topsoil, whereas dispersal limitation was dominant in the subsoil. The contribution of abiotic factors (e.g. nutrient and iron contents) and biotic factors (taxa-taxa interactions) as well as dispersal limitations to bacterial community assembly was depth specific. Concluding, the basic principles of bacterial community assembly were evaluated for the first time for a broad range of paddy soils.

Do water quality, land use, or benthic diatoms drive macroinvertebrate functional feeding groups in a subtropical mountain stream?

ABSTRACT Feeding strategies are traits that reflect the adaptation of a species to environmental conditions. Macroinvertebrates are an important primary consumer in stream food webs, but the abiotic and biotic drivers of functional feeding groups (FFGs), which are categorized based on feeding strategies, require additional clarification. The aim of our study was to quantify the contributions of abiotic factors (water quality and land use at different scales) and biotic factors (important primary producers, such as epilithic diatoms) to the variation of FFGs of macroinvertebrates in the Jinshui River, upper Han River Basin, China, a subtropical mountain river. We conducted campaigns in the Jinshui River during high stream flow (August 2009), low flow (November 2009), and normal flow (April 2010). We performed redundancy analysis and multiple factor analysis to evaluate the relationships among riparian land use at different scales, water quality, the benthic diatom community, and FFGs. We found that water quality, especially the fluoride ion (F−), metals (chromium and cadmium), and chemical oxygen demand, significantly correlated with FFGs, and that the benthic diatom community, especially Ceratoneis arcus var. linearis f. recta and Denticula tenuis, explained a high proportion of the variation in FFGs. The benthic diatom community was significantly correlated with water quality, and variations in FFGs were poorly explained by upstream riparian land use at the entire upstream scale and reach scale (2 km upstream). Further, water quality and the benthic diatom community were significantly correlated with riparian land use at the reach scale. Our findings on how the water quality, riparian land use, and diatom community influence FFGs will provide the scientific foundation for biodiversity research of macroinvertebrate FFGs, conservation of the food web, and management of the riparian zone.

Analysis of interdomain taxonomic patterns in urban street mats

Streets are constantly crossed by billions of vehicles and pedestrians. Their gutters, which convey stormwater and contribute to waste management, and are important for human health and well-being, probably play a number of ecological roles. Street surfaces may also represent an important part of city surface areas. To better characterize the ecology of this yet poorly explored compartment, we used filtration and DNA metabarcoding to address microbial community composition and assembly across the city of Paris, France. Diverse bacterial and eukaryotic taxonomic groups were identified, including members involved in key biogeochemical processes, along with a number of parasites and putative pathogens of human, animals and plants. We showed that the beta diversity patterns between bacterial and eukaryotic communities were correlated, suggesting interdomain associations. Beta diversity analyses revealed the significance of biotic factors (cohesion metrics) in shaping gutter microbial community assembly and, to a lesser extent, the contribution of abiotic factors (pH and conductivity). Co-occurrences analysis confirmed contrasting non-random patterns both within and between domains of life, specifically when comparing diatoms and fungi. Our results highlight microbial coexistence patterns in streets and reinforce the need to further explore biodiversity in urban ground transportation infrastructures.

Analysis of Magnetosome Chains in Magnetotactic Bacteria by Magnetic Measurements and Automated Image Analysis of Electron Micrographs

Magnetotactic bacteria (MTB) align along the Earth's magnetic field by the activity of intracellular magnetosomes, which are membrane-enveloped magnetite or greigite particles that are assembled into well-ordered chains. Formation of magnetosome chains was found to be controlled by a set of specific proteins in Magnetospirillum gryphiswaldense and other MTB. However, the contribution of abiotic factors on magnetosome chain assembly has not been fully explored. Here, we first analyzed the effect of growth conditions on magnetosome chain formation in M. gryphiswaldense by electron microscopy. Whereas higher temperatures (30 to 35°C) and high oxygen concentrations caused increasingly disordered chains and smaller magnetite crystals, growth at 20°C and anoxic conditions resulted in long chains with mature cuboctahedron-shaped crystals. In order to analyze the magnetosome chain in electron microscopy data sets in a more quantitative and unbiased manner, we developed a computerized image analysis algorithm. The collected data comprised the cell dimensions and particle size and number as well as the intracellular position and extension of the magnetosome chain. The chain analysis program (CHAP) was used to evaluate the effects of the genetic and growth conditions on magnetosome chain formation. This was compared and correlated to data obtained from bulk magnetic measurements of wild-type (WT) and mutant cells displaying different chain configurations. These techniques were used to differentiate mutants due to magnetosome chain defects on a bulk scale.