Bacterial Community Structure Dynamics in Meloidogyne incognita-Infected Roots and Its Role in Worm-Microbiome Interactions.

Plant parasitic nematodes such as Meloidogyne incognita have a complex life cycle, occurring sequentially in various niches of the root and rhizosphere. They are known to form a range of interactions with bacteria and other microorganisms that can affect their densities and virulence. High-throughput sequencing can reveal these interactions in high temporal and geographic resolutions, although thus far we have only scratched the surface. In this study, we have carried out a longitudinal sampling scheme, repeatedly collecting rhizosphere soil, roots, galls, and second-stage juveniles from 20 plants to provide a high-resolution view of bacterial succession in these niches, using 16S rRNA metabarcoding. Our findings indicate that a structured community develops in the root, in which gall communities diverge from root segments lacking a gall, and that this structure is maintained throughout the crop season. We describe the successional process leading toward this structure, which is driven by interactions with the nematode and later by an increase in bacteria often found in hypoxic and anaerobic environments. We present evidence that this structure may play a role in the nematode's chemotaxis toward uninfected root segments. Finally, we describe the J2 epibiotic microenvironment as ecologically deterministic, in part, due to the active bacterial attraction of second-stage juveniles.IMPORTANCE The study of high-resolution successional processes within tightly linked microniches is rare. Using the power and relatively low cost of metabarcoding, we describe the bacterial succession and community structure in roots infected with root-knot nematodes and in the nematodes themselves. We reveal separate successional processes in galls and adjacent non-gall root sections, which are driven by the nematode's life cycle and the progression of the crop season. With their relatively low genetic diversity, large geographic range, spatially complex life cycle, and the simplified agricultural ecosystems they occupy, root-knot nematodes can serve as a model organism for terrestrial holobiont ecology. This perspective can improve our understanding of the temporal and spatial aspects of biological control efficacy.

Dissecting the factors shaping fish skin microbiomes in a heterogeneous inland water system.

BACKGROUND: Fish skin microbiomes are rarely studied in inland water systems, in spite of their importance for fish health and ecology. This is mainly because fish species distribution often covaries with other biotic and abiotic factors, complicating the study design. We tackled this issue in the northern part of the Jordan River system, in which a few fish species geographically overlap, across steep gradients of water temperature and salinity. RESULTS: Using 16S rRNA metabarcoding, we studied the water properties that shape the skin bacterial communities, and their interaction with fish taxonomy. To better characterise the indigenous skin community, we excluded bacteria that were equally abundant in the skin samples and in the water samples, from our analysis of the skin samples. With this in mind, we found alpha diversity of the skin communities to be stable across sites, but higher in benthic loaches, compared to other fish. Beta diversity was found to be different among sites and to weakly covary with the dissolved oxygen, when treated skin communities were considered. In contrast, water temperature and conductivity were strong factors explaining beta diversity in the untreated skin communities. Beta diversity differences between co-occurring fish species emerged only for the treated skin communities. Metagenomics predictions highlighted the microbiome functional implications of excluding the water community contamination from the fish skin communities. Finally, we found that human-induced eutrophication promotes dysbiosis of the fish skin community, with signatures relating to fish health. CONCLUSIONS: Consideration of the background water microbiome when studying fish skin microbiomes, across varying fish species and water properties, exposes patterns otherwise undetected and highlight among-fish-species differences. We suggest that sporadic nutrient pollution events, otherwise undetected, drive fish skin communities to dysbiosis. This finding is in line with a recent study, showing that biofilms capture sporadic pollution events, undetectable by interspersed water monitoring. Video abstract.

Widespread prevalence but contrasting patterns of intragenomic rRNA polymorphisms in nematodes: Implications for phylogeny, species delimitation and life history inference.

Ribosomal RNA genes have long been a favoured locus in phylogenetic and metabarcoding studies. Within a genome, rRNA loci are organized as tandem repeated arrays and the copies are homogenized through the process of concerted evolution. However, some level of rRNA variation (intragenomic polymorphism) is known to persist and be maintained in the genomes of many species. In nematode worms, the extent of rRNA polymorphism (RP) across species and the evolutionary and life history factors that contribute to the maintenance of intragenomic RP is largely unknown. Here, we present an extensive analysis across 30 terrestrial nematode species representing a range of free-living and parasitic taxa isolated worldwide. Our results indicate that RP is common and widespread, ribosome function appears to be maintained despite mutational changes, and intragenomic variants are stable in the genome and neutrally evolving. However, levels of variation were varied widely across rRNA locus and species, with some taxa observed to lack RP entirely. Higher levels of RP were significantly correlated with shorter generation time and high reproductive rates, and population-level factors may play a role in the geographic and phylogenetic structuring of rRNA variants observed in genera such as Rotylenchulus and Pratylenchus. Although RP did not dramatically impact the clustering and recovery of taxa in mock metabarcoding analyses, the present study has significant implications for global biodiversity estimates of nematode species derived from environmental rRNA amplicon studies, as well as our understanding of the evolutionary and ecological factors shaping genetic diversity across the nematode Tree of Life.

Differential influence of molybdenum and tungsten on the growth of barley seedlings and the activity of aldehyde oxidase under salinity.

The influence of molybdenum, tungsten on germination and growth of barley Hordeum vulgare L. was studied. Results of this study revealed the differential effect of heavy metals on seedlings growth. Exogenous molybdenum treatment stimulated the growth of seedlings. The addition of the metal significantly stimulated root elongation. Contrastingly, the addition of tungsten resulted in increased seed germination and inhibits the growth of seedlings. The negative effect of tungsten on the growth of barley was more profound for roots of plants. In addition, the influence of metals on the growth of plants was also tested in saline conditions. It is shown that under salinity stress plant growth drastically decreased in presence of tungsten. Results of this study showed that activity of molybdenum-containing aldehyde oxidase (AO; EC 1.2.3.1) was also significantly affected by metals. The activity of AO in leaves and roots enhanced with increasing concentrations of molybdate, while tungstate treatment inhibited the enzyme activity. Perhaps, the differential influence of molybdenum and tungsten on the growth of barley is a direct effect of metals on aldehyde oxidase activity in plants. Moreover, the intense negative effect of tungsten treatment on barley growth under salinity conditions emphasizes an important role of aldehyde oxidase in plant resistance to stress factors.

The involvement of ROS producing aldehyde oxidase in plant response to Tombusvirus infection.

The influence of Tomato bushy stunt virus (TBSV) infection on the activity and isoformic composition of aldehyde oxidase and catalase in Nicotiana benthamiana plants was investigated. It was shown that the infection of plants with TBSV results in enhancement of leaf aldehyde oxidase (AO) isoforms AO2 and AO3. Significantly enhanced levels of superoxide radical producing activity of AO isoforms were also detected. This is the first demonstration of involvement of plant AO in defense mechanisms against viral infection. In addition, the infection caused an increased accumulation of hydrogen peroxide, compared to mock-inoculated plants. The virus infection resulted in increased activity of catalase (CAT) and superoxide dismutase (SOD) in roots and leaves of N. benthamiana. Moreover, activation of two additional CAT isoforms was observed in the leaves of plants after virus inoculation. Our findings indicate that the virus infection significantly affects enzymes responsible for the balance of ROS accumulation in plant tissue in response to pathogen attack.