Structure and variation of root-associated microbiomes of potato grown in alfisol.

Root-associated fungi and bacteria play a pivotal role in the plant-soil ecosystem by influencing both plant growth and immunity. The aim of this study was to unravel the biodiversity of the bacterial and fungal rhizosphere (RS) and rhizoplane (RP) microbiota of Zhukovskij rannij potato (Solanum tuberosum L.) cultivar growing in the Alfisol of Tatarstan, Russia. To assess the structure and diversity of microbial communities, we employed the 16S rRNA and internal transcribed spacer gene library technique. Overall, sequence analysis showed the presence of 3982 bacterial and 188 fungal operational taxonomic units (OTUs) in the RP, and 6018 bacterial and 320 fungal OTUs for in the RS. Comparison between microbial community structures in the RS and RP showed significant differences between these compartments. Biodiversity was higher in the RS than in the RP. Although members of Proteobacteria (RS-59.1 ± 4.9%; RP-54.5 ± 9.2%), Bacteroidetes (RS-23.19 ± 10.2%; RP-34.52 ± 10.4%) and Actinobacteria (RS-11.55 ± 4.9%; RP-7.7 ± 5.1%) were the three most dominant phyla, accounting for 94-98% of all bacterial taxa in both compartments, notable variations were observed in the primary dominance of classes and genera in RS and RP samples. In addition, our results demonstrated that the potato rhizoplane was significantly enriched with the genera Flavobacterium, Pseudomonas, Acinetobacter and other potentially beneficial bacteria. The fungal community was predominantly inhabited by members of the Ascomycota phylum (RS-81.4 ± 8.1%; RP-81.7 ± 5.7%), among which the genera Fusarium (RS-10.34 ± 3.41%; RP-9.96 ± 4.79%), Monographella (RS-7.66 ± 4.43%; RP-9.91 ± 5.87%), Verticillium (RS-4.6 ± 1.43%; RP-8.27 ± 3.63%) and Chaetomium (RS-4.95 ± 2.07%; RP-8.33 ± 4.93%) were particularly abundant. Interestingly, potato rhizoplane was significantly enriched with potentially useful fungal genera, such as Mortierella and Metacordiceps. A comparative analysis revealed that the abundance of Fusarium (a cosmopolitan plant pathogen) varied significantly depending on rotation variants, indicating a possible control of phytopathogenic fungi via management-induced shifts through crop rotational methods. Analysis of the core microbiome of bacterial and fungal community structure showed that the formation of bacterial microbiota in the rhizosphere and rhizoplane is dependent on the host plant.

Fungal, Bacterial, and Archaeal Diversity in the Digestive Tract of Several Beetle Larvae (Coleoptera).

Interpretation of how partnerships between fungi, bacteria, archaea, and insects are maintained through the life of the hosts is a big challenge within the framework of symbiosis research. The main goal of this work was to characterize the gut microbiota in larvae of several Coleoptera species using sequencing of the bacterial and archaeal 16S rRNA genes and fungal internal transcribed spacer (ITS) region. Thus, larvae with various food preferences, including Amphimallon solstitiale, Oryctes nasicornis, Cucujus cinnaberinus, Schizotus pectinicornis, Rhagium mordax, and Rhagium inquisitor, were thoroughly investigated in this work. We revealed an association of these beetle species mainly with four bacterial phyla, Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes, as well as with three fungal phyla, Ascomycota, Zygomycota, and Basidiomycota, but microbial communities varied depending on the beetle host, individual organism, and surrounding environment. Moreover, archaea within the phyla Euryarchaeota and Crenarchaeota in the hindgut content of O. nasicornis and A. solstitiale were additionally detected. The identified microbial communities suggest their potential role in the exploitation of various resources, providing nutritional needs for the host organism. These microorganisms can also represent a valuable source of novel metabolic capacities for their application in different biotechnologies.

Comparison of anaerobic digestion strategies of nitrogen-rich substrates: Performance of anaerobic reactors and microbial community diversity.

In the present study, the application of different operating strategies on performance of three continuous stirred tank reactors digesting chicken manure at mesophilic temperature and constant organic loading rate (OLR) of 3.5gVSL-1d-1 was investigated. Control reactor (RC) and reactor (RH) with the decreasing hydraulic retention time (HRT) had the comparable specific biogas production (SBP) with maximum values of 334-351mLg-1VS (added) during days 84-93, while the SBP from reactor with zeolites (RZ) was higher and achieved 426-432mLg-1VS (added). Attachments of microorganisms to zeolite particles as the operational environment, exchanged cations released from zeolites as well as lower total ammonium nitrogen (TAN) levels observed in RZ (6.2-6.3gL-1; days 71-93) compared to RC (6.6-6.9gL-1; days 71-93) resulted in a more effective process in RZ. Moreover, microbial community structure and dynamics were comprehensively characterized using Illumina sequencing, pyrosequencing and T-RFLP analysis of 16SrRNA genes. Methanogenic archaeal activity was additionally assessed by the expressed mcrA genes encoding the alpha subunit of methyl-CoM reductase. Within the major class Clostridia, Caldicoprobacter, Alkaliphilus, Gallicola, Sporanaerobacter and Tepidimicrobium spp. were the notable bacteria developed during operation of all tested reactors. Archaeal communities were dominated by methanogens belonging to the genus Methanosarcina followed by the genus Methanoculleus during the experimental period. Results of this study indicate that attachment of microorganisms to the zeolite particles as the operational environment might have led to the higher microbial activity at high ammonia concentrations.

Microbial community diversity in anaerobic reactors digesting turkey, chicken, and swine wastes.

The microbial community structures of two continuous stirred tank reactors digesting turkey manure with pine wood shavings as well as chicken and swine manure were investigated. The reactor fed with chicken/swine wastes displayed the highest organic acids concentration (up to 15.2 g/l) and ammonia concentration (up to 3.7 g/l ammonium nitrogen) and generated a higher biogas yield (up to 366 ml/g(VS)) compared with the reactor supplied with turkey wastes (1.5- 1.8 g/l of organic acids and 1.6-1.7 g/l of ammonium levels; biogas yield was up to 195 ml/g(VS)). The microbial community diversity was assessed using both sequencing and profiling terminal restriction fragment length polymorphisms of 16S rRNA genes. Additionally, methanogens were analyzed using methyl coenzyme M reductase alpha subunit (mcrA) genes. The bacterial community was dominated by members of unclassified Clostridiales with the prevalence of specific clostridial phylotypes in each reactor, indicating the effect of the substrate type on the community structure. Of the methanogenic archaea, methanogens of the genus Methanosarcina were found in high proportions in both reactors with specific methanosarcinas in each reactor, whereas the strict hydrogenotrophic methanogens of Methanoculleus sp. were found at significant levels only in the reactor fed with chicken/swine manure (based on the analyses of 16S rRNA gene). This suggests that among methanogenic archaea, Methanosarcina species which have different metabolic capabilities, including aceticlastic and hydrogenotrophic methanogenesis, were mainly involved in anaerobic digestion of turkey wastes.