Phylogenomic analysis of Pseudomonas nitroreducens strains FY43 and FY47

Proper identification of strain is essential in understanding the ecology of a bacteria species. The classification of Pseudomonas nitroreducens is still being questioned and revised until now. The novel P. nitroreducens strains FY43 and FY47 used in this study have been reported to show a high level of tolerance to glyphosate. In this study, next-generation sequencing (NGS) and whole genome analysis were used to clarify the delineation of the species. Whole genome analysis showed that P. nitroreducens strains FY43 and FY47 shared high homology to five reference genomes of P. nitroreducens: strain B, Aramco J, NBRC 12694, DF05, and TX01. Phylogenomic and phylogenetic analysis (average nucleotide identity based on BLAST (ANIb), genome-to-genome distance (GGDC) analysis) showed that both P. nitroreducens strains FY43 and FY47 are Pseudomonas nitroreducens members. However, strains DF05 and TX01 were not correctly assigned at the species level for all the analyses. The P. nitroreducens strain DF05 and TX01 should be further investigated for their classification as the correct species classification is the prerequisite for future diversity studies.

Genetic Diversity Studies in Mungbean (Vigna radiata L. Wilczek) Germplasm

An investigation was carried out to estimate the genetic divergence for twenty characters in 50 genotypes of greengram [Vigna radiata (L.) Wilczek] using Mahalanobis's D2 statistic and total of eight clusters were formed. The highest number of genotypes were found in cluster II containing sixteen genotypes followed by cluster I with thirteen genotypes, cluster IV with ten genotypes, cluster VI with five genotypes, cluster VIII with three genotypes and clusters III, V and VII with only one genotype. Highest intra-cluster distance was observed for cluster IV (87.54) and lowest intra cluster distance was observed for clusters III, V and VII. The highest inter-cluster distance was observed between cluster IV and VIII (285.11),while the lowest inter cluster distance was observed between cluster VI and VII (251.29). Among the characters studied, phenols content contributed the maximum (32.57 %) towards the diversity. The genotypes present in the clusters V (COGG-13-19) and VII (LGG-544) showed high seed yield performance so, cross obtained between these genotypes will give better performance for yield. The genotypes in the cluster VI (GGG-1, GGG-1-1, IPM-2-14, WGG-42, EC-396117) and cluster III (AGG-35) exhibited resistance to YMV. Hence, the crosses among cluster V, VII, VI and III would give high seed yield along with YMV disease resistance.

Moth species richness in an upland tropical rainforest: A citizen scientist assisted study

Diversity studies on moths in Australia are rare, presenting various shortfalls in knowledge that impedes and understanding of their biodiversity values and their conservation. In particular, the Wet Tropics of Australia deserves attention, given the paucity of systematic moth surveys in the region and its World Heritage Area status. To fill this knowledge gap, we conducted a study to observe moths on 191 nights over a main one-year survey period at an upland rainforest locality, and uploaded all observations on iNaturalist. We also compiled other incidental observations in the general locality by other observers and observations outside the survey period. In total, we document 4,434 observations of moths represented by 1041 distinct moth morphospecies. Of these, 703 are formally named species of moths, 146 to genus and 255 to higher taxonomic designations above genus level. Despite the rather intensive main survey effort, our results suggest that we have yet to reach a plateau in documenting the moth species richness of the locality. Using this study as a model, we show that the iNaturalist platform serves as an effective means to document and digitally curate biodiversity values at a locality, whilst providing complete data transparency and enabling broader community engagement of citizen scientists. We recommend the use of iNaturalist for future moth inventories, and as a resource for follow up meta-analyses of regional moth diversity and distributions.

Geobiology of Andean Microbial Ecosystems Discovered in Salar de Atacama, Chile

The Salar de Atacama in the Chilean Central Andes harbors unique microbial ecosystems due to extreme environmental conditions, such as high altitude, low oxygen pressure, high solar radiation, and high salinity. Combining X-ray diffraction analyses, scanning electron microscopy and molecular diversity studies, we have characterized twenty previously unexplored Andean microbial ecosystems in eight different lakes and wetlands from the middle-east and south-east regions of this salt flat. The mats and microbialites studied are mainly formed by calcium carbonate (aragonite and calcite) and halite, whereas the endoevaporites are composed predominantly of gypsum and halite. The carbonate-rich mats and microbialites are dominated by Bacteroidetes and Proteobacteria phyla. Within the phylum Proteobacteria, the most abundant classes are Alphaproteobacteria, Gammaproteobacteria and Deltaproteobacteria. While in the phylum Bacteroidetes, the most abundant classes are Bacteroidia and Rhodothermia. Cyanobacteria, Chloroflexi, Planctomycetes, and Verrucomicrobia phyla are also well-represented in the majority of these systems. Gypsum endoevaporites, on the contrary, are dominated by Proteobacteria, Bacteroidetes, and Euryarchaeota phyla. The Cyanobacteria phylum is also abundant in these systems, but it is less represented in comparison to mats and microbialites. Regarding the eukaryotic taxa, diatoms are key structural components in most of the microbial ecosystems studied. The genera of diatoms identified were Achnanthes, Fallacia, Halamphora, Mastogloia, Navicula, Nitzschia, and Surirella. Normally, in the mats and microbialites, diatoms form nano-globular carbonate aggregates with filamentous cyanobacteria and other prokaryotic cells, suggesting their participation in the mineral precipitation process. This work expands our knowledge of the microbial ecosystems inhabiting the extreme environments from the Central Andes region, which is important to ensure their protection and conservation.

Influence of DNA extraction kits on the fungal DNA metabarcoding for freshwater environmental DNA

Background: Environmental DNA (eDNA) metabarcoding is a rapidly expanding technique for efficient biodiversity monitoring, especially of animals. Recently, the usefulness of aquatic eDNA in monitoring the diversity of both terrestrial and aquatic fungi has been suggested. In eDNA studies, different experimental factors, such as DNA extraction kits or methods, can affect the subsequent analyses and the results of DNA metabarcoding. However, few methodological studies have been carried out on eDNA of fungi, and little is known about how experimental procedures can affect the results of biodiversity analysis. In this study, we focused on the effect of the DNA extraction method on fungal DNA metabarcoding using freshwater samples obtained from rivers and lakes. Methods: DNA was extracted from freshwater samples using the DNeasy PowerSoil kit, which is mainly used to extract microbial DNA from soil, and the DNeasy Blood & Tissue kit, which is commonly used for eDNA studies on animals. We then compared PCR inhibition and fungal DNA metabarcoding results [i.e., operational taxonomic unit (OTU) number and composition] of the extracted samples. Results: No PCR inhibition was detected in any of the samples, and no significant differences in the number of OTUs and OTU compositions were detected between the samples processed using different kits. These results indicate that both DNA extraction kits may provide similar diversity results for the river and lake samples evaluated in this study. Therefore, it may be possible to evaluate the diversity of fungi using a unified experimental method, even with samples obtained for diversity studies on other taxa such as those of animals.