Trichovariability in rhizosphere soil samples and their biocontrol potential against downy mildew pathogen in pearl millet

The present work is aimed to examine the genetic variability and the distribution pattern of beneficial Trichoderma spp. isolated from rhizosphere samples and their mode of action in improving the plant health. A total of 131 suspected fungi were isolated from the rhizospheric soil and 91 isolates were confirmed as Trichoderma spp. T. asperellum and T. harzianum were found high in the frequency of occurrence. Genetic diversity analysis using RAPD and ISSR revealed the diverse distribution pattern of Trichoderma spp. indicating their capability to adapt to broad agroclimatic conditions. Analysis of genetic diversity using molecular markers revealed intra-species diversity of isolated Trichoderma spp. The frequency of pearl millet (PM) root colonization by Trichoderma spp. was found to be 100%. However, they showed varied results for indole acetic acid, siderophore, phosphate solubilization, β-1,3-glucanase, chitinase, cellulase, lipase, and protease activity. Downy mildew disease protection studies revealed a strong involvement of Trichoderma spp. in direct suppression of the pathogen (mean 37.41) in the rhizosphere followed by inducing systemic resistance. Our findings highlights the probable distribution and diversity profile of Trichoderma spp. as well as narrate the possible utilization of Trichoderma spp. as microbial fungicides in PM cultivation across different agroclimatic zones of India.

Peeling the Layers of Caddisfly Diversity on a Longitudinal Gradient in Karst Freshwater Habitats Reveals Community Dynamics and Stability

Freshwater biodiversity is facing a severe crisis due to many human impacts, yet the diversity dynamics of freshwater communities and possibilities of assessing these are vastly unexplored. We aimed at emphasizing different aspects of portraying diversity of a species-rich, aquatic insect group (caddisflies; Trichoptera) across four different habitats in an anthropogenically unimpacted, connected karst barrage lake/riverine system. To define diversity, we used common indices with pre-set sensitivity to species abundance/dominance; i.e., sensitivity parameter (species richness, Shannon, Simpson, Berger-Parker) and diversity profiles based on continuous gradients of this sensitivity parameter: the naïve and non-naïve diversity profiles developed by Leinster and Cobbold. The non-naïve diversity profiles show diversity profiles with regard to the similarity among species in terms of ecological traits and preferences, whereas the naïve diversity profile is called mathematically “naïve” as it assumes absolute dissimilarity between species that is almost never true. The commonly used indices and the naïve diversity profile both ranked the springs as least diverse and tufa barriers as most diverse. The non-naïve diversity profiles based on similarity matrices (using feeding behavior and stream zonation preferences of species), showed even greater differences between these habitats, while ranking stream habitats close together, regardless of their longitudinal position. We constructed the Climate Score index (CSI) in order to assess how diversity and species’ vulnerability project the community’s resistance and/or resilience to climate change. The CSI ranked the springs as most vulnerable, followed by all habitats longitudinally placed below them. We highlight the importance of integrating ecological information into biodiversity and vulnerability assessment of freshwater communities.

Dominance Hierarchies, Diversity and Spatial Connect of Crops in Banana Based High Range Home Gardens

Home gardens are a time tested food production system which can be projected as a promise to the future to mitigate the issues related to the global food security crisis. The home gardens in Kerala are an integral part of the rich tradition which impart a dominant role in livelihood security of the people. The diversity profile of traditional homegardens of high range area and its spatial patterns were investigated in the present study revealed that a mean Shannon and Wiener diversity index (H) of 2.185 was recorded which denoted a dwindling trend in species diversity in banana based high range home gardens of Idukki. An appraisal of the diversity of crops revealed that the highest diversity was recorded in spices (H=1.425) and was on par with fruit crops (H=1.339) whereas lowest was noted on fodder crops (H= 0.054) followed by medicinal plants (H=0.197). Furthermore, the mean total diversity index exhibited a positive significant correlation with the total area of the home garden with a correlation coefficient of 0.621 which signified the importance of spatial dimensions in determining the diversity profile of the home gardens.

Towards a unifying diversity-area relationship (DAR) of species- and gene-diversity

AimThe microbiome as a biogeographic entity can be investigated, to the minimum, from two perspectives: one is the spatial/temporal distribution of species (or any level of the operational taxonomic unit or OTU) diversity, and another is the spatial/temporal distribution of metagenomic gene diversity. Both are necessary for comprehensive understanding of the taxonomical, ecological, evolutionary and functional aspects of the microbiome biogeography. Here we propose to investigate the metagenomic diversity-area relationship (m-DAR), which is a transformation of the species-DAR (s-DAR) that extended the classic SAR (species-area relationship) by replacing the species richness with general species diversity measured in Hill numbers.InnovationThe m-DAR and s-DAR, using the same mathematical models, offer a unifying tool for investigating the biogeography of microbiome from ecological, metagenomic and functional perspectives. Specifically, we investigate m-DAR of the human gut metagenome in terms of the MG (metagenomic gene) and MFGC (metagenome functional gene cluster) respectively, by sketching out the DAR-profile, PDO (pair-wise diversity overlap) profile, MAD (maximal accrual diversity) profile, and RIP (ratio of individual- to population-diversity) profile at each scale. These profiles constitute our unifying DAR toolset and can be applied to any microbiomes beyond the human gut microbiome.Main conclusionsWe demonstrate the construction and applications of the m-DAR and its associated four profiles with six large datasets of the human gut metagenomes including three microbiome-associated diseases (obesity, diabetes, IBD) and their healthy controls, supported with randomization tests to determine the differences between healthy and diseased treatments in their m-DAT parameters. Theoretically, our study presents a successful case to demonstrate the feasibility of unifying systematic biogeography vs. evolutionary biogeography, of an inclusive biogeography of plants, animal and microbes. Practically, our approach offers an important tool for investigating the spatial scaling of human metagenome diversity in a population (cohort) and its relationship with individual-level diversity.

Dynamic Succession of Microbiota during Ensiling of Whole Plant Corn Following Inoculation with Lactobacillus buchneri and Lactobacillus hilgardii Alone or in Combination

Lactic acid bacteria (LAB) used as silage additives have been shown to improve several fermentation parameters, including aerobic stability. Inoculation with a combination of Lactobacillus buchneri NCIMB40788 and Lactobacillus hilgardii CNCM-I-4785, contributes to an increase in aerobic stability, compared to each strain inoculated independently. To understand the mode of action of the combination on the LAB community, a fermentation-kinetic study was performed on corn. Four treatments, Control, Lb. buchneri, Lb. hilgardii, and a combination of the two strains, were fermented 1, 2, 4, 8, 16, 32, and 64 days. Corn silage inoculated by both strains had a lactate:acetate ratio of 0.59 after 64 days and a higher concentration of lactate than Lb. buchneri. Analysis of the microbiota by 16S and ITS amplicon metasequencing demonstrated that inoculation led to lower bacterial diversity after 1 day, from 129.4 down to 40.7 observed operational taxonomic units (OTUs). Leuconostocaceae represented the dominant population by day 1, with 48.1%. Lactobacillaceae dominated the succession by day 4, with 21.9%. After 32 days, inoculation by both strains had the lowest bacterial alpha diversity level, with 29.0 observed OTUs, compared to 61.3 for the Control. These results confirm the increased fermentation efficiency when the two Lactobacillus strains are co-inoculated, which also led to a specific yeast OTUs diversity profile, with Hannaella as the main OTU.

Station and train surface microbiomes of Mexico City’s metro (subway/underground)

The metro is one of the more representative urban systems of Mexico City, and it transports approximately 4.5 million commuters every day. Large crowds promote the constant exchange of human and environmental microbes. In this study, we determined the bacterial diversity profile of the Mexico City subway by massive sequencing of the 16S rRNA gene. We identified a total of 50,197 operative taxonomic units (OTUs) and 1058 genera. The metro microbiome was dominated by the phylum Actinobacteria and by the genera Propionibacterium (15%) (P. acnes 13%), Corynebacterium (13%), Streptococcus (9%), and Staphylococcus (5%) (S. epidermidis; 4%), reflecting the microbe composition of normal human skin. The metro microbial sources were skin, dust, saliva, and vaginal, with no fecal contribution detected. A total of 420 bacterial genera were universal to the twelve metro lines tested, and they contributed to 99.10% of the abundance. The large OTUs number are probably reflecting the vast human influx, while selection from hosts and environments are constraining the genera diversity, shown by the OTUs to genus ratio. Finally, this study shows that the microbial composition of the Mexico City subway comes from a mixture of environmental and human sources and that commuters are exposed to normal human microbiota.

The intertidal gastropods (Gastropoda: Mollusca) diversity and taxa distribution in Alas Purwo National Park, East Java, Indonesia

Susintowati, Puniawati N, Poedjirahajoe, Handayani NSN, Hadisusanto S. 2019. The intertidal gastropods (Gastropoda: Mollusca) diversity and taxa distribution in Alas Purwo National Park, East Java, Indonesia. Biodiversitas 20: 2016-2027. Gastropods play an essential role in the ecosystem and can be used as bioindicators of environmental pollution. Understanding of their behavior, habitat, and distribution, and how these factors evolve, is crucial. This paper aimed to describe the diversity of the gastropod community and their spatial taxa distribution, based on the specimen frequency across all observed samples, in the diverse environment of Alas Purwo National Park (APNP), East Java, Indonesia. We studied eight beaches and two mangroves areas, and the study areas of the intertidal zone divided into upper, middle, and lower zones towards the sea. The purposive sampling was used to determine the locations and multi-plot quadrats for observations. The diversity of gastropods was elucidated by using the Shannon and Simpson indexes, while the Morisita index was applied for analyzing their spatial distribution pattern. However, the correspondence analysis and principal component analysis were performed using the software of PAST 3.22 for describing the diversity profile and individual rarefaction of gastropods together with environmental quality. There were three beach types: rocky, sandy, and muddy beaches were found in APNP. The highest diversity index (H’) was found on Pancur beach: H’ = 3.271, D = 0.947 of 67 species. The spatial distribution pattern of gastropods species was weakly clumped to random, with Ip: 0.165 - 0.016. Gastropods, both predators and scavengers, were distributed from the upper to lower zones. The distribution of gastropods in APNP is mostly in type B. These results expand our knowledge of gastropods diversity and distribution of Indonesia’s beach and can contribute to the future environmental assessments of biodiversity of tropical intertidal zones worldwide.