Molecular approaches to study the insect gut symbiotic microbiota at the ＇omics＇ age

Insect gut symbiotic microbiota play essential roles in the growth, development, pathogenesis and environmental adaptation of host insects. The molecular and systems level analysis of insect gut symbiotic microbial community will allow us to discover novel biocatalysts for biomass deconstruction and to develop innovative strategies for pest management. We hereby review the various molecular biology techniques as applied to insect gut symbiont analysis. This review aims to serve as an informative resource for experimental design and research strategy development in the field. We first discuss various strategies for sample preparation and their pros and cons. The traditional molecular techniques like DGGE, RFLP and FISH are covered with respect to how they are applied to study the composition, diversity and dynamics of insect gut symbiotic microbiota. We then focus on the various ＇ omics＇ techniques. The metagenome analysis together with the recent advancements in next-generation sequencing will provide enormous sequencing information, allowing in-depth microbial diversity analysis and modeling of pathways for biological processes such as biomass degradation. The metagenome sequencing will also enable the study of system dynamics and gene expression with metatranscriptome and metaproteome methods. The integration of different ＇omics＇ level data will allow us to understand how insect gut works as a system to carry out its functions. The molecular and systems-level understanding will also guide the reverse design of next-generation biorefinery.

Plant-associated fungal communities in the light of meta’omics

Approaches for the cultivation-independent analysis of microbial communities are summarized as meta’omics,which predominantly includes metagenomic,-transcriptomic,-proteomic and-metabolomic studies.These have shown that endophytic,root-associated and soil fungal communities are strongly shaped by associated plant species.The impact of plant identity on the composition of its litterssociated fungal community remains to be disentangled from the impact of litter chemistry.The composition of the plant community also shapes the fungal community.Most strikingly,adjacent plant species may share mycorrhizal symbionts even if the plants usually have different types of mycorrhizal fungi associated with them(ectomycorrhizal,ericoid and arbuscular mycorrhizal fungi).Environmental parameters weakly explain fungal community composition globally,and their effect is inconsistent at local and regional scales.Decrease in similarity among communities with increasing distance(i.e.distance decay)has been reported from local to global scales.This pattern is only exceptionally caused by spatial dispersal limitation of fungal propagules,but mostly due to the inability of the fungi to establish at the particular locality(i.e.environmental filtering or competitive exclusion).Fungal communities usually undergo pronounced seasonal changes and also differ between consecutive years.This indicates that development of the communities is usually not solely cyclic.Meta’omic studies challenge the classical view of plant litter decomposition.They show that mycorrhizal and(previously)endophytic fungi may be involved in plant litter decomposition and only partly support the idea of a succession from an Ascomycota to a Basidiomycota-dominated community.Furthermore,vertical separation of saprotrophic and mycorrhizal species in soil and sequential degradation from easily accessible to‘recalcitrant’plant compounds,such as lignin,can probably not be generalized.The current models of litter decomposition may therefore have to be eventually refined for certain ecosystems and environmental conditions.To gain deeper insights into fungal ecology,a meta’omic study design is outlined which focuses on environmental processes,because fungal communities are usually taxonomically diverse,but functionally redundant.This approach would initially identify dynamics of chemical shifts in the host and/or substrate by metametabolomics.Detected shifts would be subsequently linked to microbial activity by correlation with metatranscriptomic and/or metaproteomic data.A holistic trait-based approach might finally identify factors shaping taxonomic composition in communities against the dynamics of the environmental process(es)they are involved in.

Metabolic tuning of a stable microbial community in the surface oligotrophic Indian Ocean revealed by integrated meta-omics

Understanding the mechanisms,structuring microbial communities in oligotrophic ocean surface waters remains a major ecological endeavor.Functional redundancy and metabolic tuning are two mechanisms that have been proposed to shape microbial response to environmental forcing.However,little is known about their roles in the oligotrophic surface ocean due to less integrative characterization of community taxonomy and function.Here,we applied an integrated meta-omics-based approach,from genes to proteins,to investigate the microbial community of the oligotrophic northern Indian Ocean.Insignificant spatial variabilities of both genomic and proteomic compositions indicated a stable microbial community that was dominated by Prochlorococcus,Synechococcus,and SAR11.However,fine tuning of some metabolic functions that are mainly driven by salinity and temperature was observed.Intriguingly,a tuning divergence occurred between metabolic potential and activity in response to different environmental perturbations.Our results indicate that metabolic tuning is an important mechanism for sustaining the stability of microbial communities in oligotrophic oceans.In addition,integrated meta-omics provides a powerful tool to comprehensively understand microbial behavior and function in the ocean.