Editorial: Advances in the Understanding of the Commensal Eukaryota and Viruses of the Herbivore Gut

Herbivores play an important role in the survival of humanity, contributing food and textiles, as well as social and economic value. For decades, optimizing the productivity, health, welfare, and environmental footprint of herbivorous animals, particularly ruminant livestock, has been the subject of an extensive, global research effort. Much of this research effort has focused on the herbivore gut. The specialized nature of the herbivore digestive tract and its resident microbes enables the breakdown of highly fibrous plant materials, which are unable to be utilized by omnivores and carnivores. In recent years, the bacteria and methanogenic archaea have been the major focus of research efforts, with the other gut microbes being understudied in comparison

Horizontal Gene Transfer as an Indispensable Driver for Evolution of Neocallimastigomycota into a Distinct Gut-Dwelling Fungal Lineage

Survival and growth of the anaerobic gut fungi (AGF; Neocallimastigomycota) in the herbivorous gut necessitate the possession of multiple abilities absent in other fungal lineages. We hypothesized that horizontal gene transfer (HGT) was instrumental in forging the evolution of AGF into a phylogenetically distinct gut-dwelling fungal lineage. The patterns of HGT were evaluated in the transcriptomes of 27 AGF strains, 22 of which were isolated and sequenced in this study, and 4 AGF genomes broadly covering the breadth of AGF diversity. We identified 277 distinct incidents of HGT in AGF transcriptomes, with subsequent gene duplication resulting in an HGT frequency of 2 to 3.5% in AGF genomes. The majority of HGT events were AGF specific (91.7%) and wide (70.8%), indicating their occurrence at early stages of AGF evolution. The acquired genes allowed AGF to expand their substrate utilization range, provided new venues for electron disposal, augmented their biosynthetic capabilities, and facilitated their adaptation to anaerobiosis. The majority of donors were anaerobic fermentative bacteria prevalent in the herbivorous gut. This study strongly indicates that HGT indispensably forged the evolution of AGF as a distinct fungal phylum and provides a unique example of the role of HGT in shaping the evolution of a high-rank taxonomic eukaryotic lineage.IMPORTANCE The anaerobic gut fungi (AGF) represent a distinct basal phylum lineage (Neocallimastigomycota) commonly encountered in the rumen and alimentary tracts of herbivores. Survival and growth of anaerobic gut fungi in these anaerobic, eutrophic, and prokaryote-dominated habitats necessitates the acquisition of several traits absent in other fungal lineages. We assess here the role of horizontal gene transfer as a relatively fast mechanism for trait acquisition by the Neocallimastigomycota postsequestration in the herbivorous gut. Analysis of 27 transcriptomes that represent the broad diversity of Neocallimastigomycota identified 277 distinct HGT events, with subsequent gene duplication resulting in an HGT frequency of 2 to 3.5% in AGF genomes. These HGT events have allowed AGF to survive in the herbivorous gut by expanding their substrate utilization range, augmenting their biosynthetic pathway, providing new routes for electron disposal by expanding fermentative capacities, and facilitating their adaptation to anaerobiosis. HGT in the AGF is also shown to be mainly a cross-kingdom affair, with the majority of donors belonging to the bacteria. This study represents a unique example of the role of HGT in shaping the evolution of a high-rank taxonomic eukaryotic lineage

PCR and Omics Based Techniques to Study the Diversity, Ecology and Biology of Anaerobic Fungi:Insights, Challenges, and Opportunities

Anaerobic fungi (phylum Neocallimastigomycota) are common inhabitants of the digestive tract of mammalian herbivores, and in the rumen, can account for up to 20% of the microbial biomass. Anaerobic fungi play a primary role in the degradation of lignocellulosic plant material. They also have a syntrophic interaction with methanogenic archaea, which increases their fiber degradation activity. To date, nine anaerobic fungal genera have been described, with further novel taxonomic groupings known to exist based on culture-independent molecular surveys. However, the true extent of their diversity may be even more extensively underestimated as anaerobic fungi continue being discovered in yet unexplored gut and non-gut environments. Additionally many studies are now known to have used primers that provide incomplete coverage of the Neocallimastigomycota. For ecological studies the internal transcribed spacer 1 region (ITS1) has been the taxonomic marker of choice, but due to various limitations the large subunit rRNA (LSU) is now being increasingly used. How the continued expansion of our knowledge regarding anaerobic fungal diversity will impact on our understanding of their biology and ecological role remains unclear; particularly as it is becoming apparent that anaerobic fungi display niche differentiation. As a consequence, there is a need to move beyond the broad generalization of anaerobic fungi as fiber-degraders, and explore the fundamental differences that underpin their ability to exist in distinct ecological niches. Application of genomics, transcriptomics, proteomics and metabolomics to their study in pure/mixed cultures and environmental samples will be invaluable in this process. To date the genomes and transcriptomes of several characterized anaerobic fungal isolates have been successfully generated. In contrast, the application of proteomics and metabolomics to anaerobic fungal analysis is still in its infancy. A central problem for all analyses, however, is the limited functional annotation of anaerobic fungal sequence data. There is therefore an urgent need to expand information held within publicly available reference databases. Once this challenge is overcome, along with improved sample collection and extraction, the application of these techniques will be key in furthering our understanding of the ecological role and impact of anaerobic fungi in the wide range of environments they inhabit

Potential of airborne hyperspectral data for geo-exploration over parts of different geological/metallogenic provinces in India based on AVIRIS-NG observations

In this article, we discuss the potential of airborne hyperspectral data in mapping host rocks of mineral deposits and surface signatures of mineralization using AVIRIS-NG data of a few important geological provinces in India. We present the initial results from the study sites covering parts of northwest India, as well as the Sittampundi Layered Complex (SLC) of Tamil Nadu and the Wajrakarur Kimberlite Field (WKF) of Andhra Pradesh from southern India. Modified spectral summary parameters, originally designed for MRO-CRISM data analysis, have been implemented on AVIRIS-NG mosaic of Jahazpur, Ra-jasthan for the automatic detection of phyllosilicates, carbonates and Fe–Mg-silicates. Spectral analysis over Ambaji and the surrounding areas indicates the pres-ence of calcite across much of the study area with kao-linite occurring as well in the north and east of the study area. The deepest absorption features at around 2.20 and 2.32 μm and integrated band depth were used to identify and map the spatial distribution of phyllosilicates and carbonates. Suitable thresholds of band depths were applied to map prospective zones for marble exploration. The data over SLC showed potential of AVIRIS-NG hyperspectral data in detecting mafic cumulates and chromitites. We also have demonstrated the potential of AVIRIS-NG data in detecting kimberlite pipe exposures in parts of WKF