A biogeographic 16S rRNA survey of bacterial communities of ureolytic biomineralization from California public restrooms

In this study, we examined the total bacterial community associated with ureolytic biomineralization from urine drainage systems. Biomineral samples were obtained from 11 California Department of Transportation public restrooms fitted with waterless, low-flow, or conventional urinals in 2019. Following high throughput 16S rRNA Illumina sequences processed using the DADA2 pipeline, the microbial diversity assessment of 169 biomineral and urine samples resulted in 3,869 reference sequences aggregated as 598 operational taxonomic units (OTUs). Using PERMANOVA testing, we found strong, significant differences between biomineral samples grouped by intrasystem sampling location and urinal type. Biomineral microbial community profiles and alpha diversities differed significantly when controlling for sampling season. Observational statistics revealed that biomineral samples obtained from waterless urinals contained the largest ureC/16S gene copy ratios and were the least diverse urinal type in terms of Shannon indices. Waterless urinal biomineral samples were largely dominated by the Bacilli class (86.1%) compared to low-flow (41.3%) and conventional samples (20.5%), and had the fewest genera that account for less than 2.5% relative abundance per OTU. Our findings are useful for future microbial ecology studies of urine source-separation technologies, as we have established a comparative basis using a large sample size and study area.

Reclassification of Gall Midges (Diptera: Cecidomyiidae: Cecidomyiini) from Amaranthaceae, with Description of Ten New Species Based on an Integrative Taxonomic Study

The genus Halodiplosis includes 99 species restricted to host-plants of the Amaranthaceae, virtually all of which are from Central Asia. The discovery of numerous undescribed species putatively belonging to this genus in Israel instigated an exhaustive review of the original descriptions of all known species in this genus. This study revealed that the generic concept of Halodiplosis and some of the genera synonymized under it should be redefined based on morphological and life-history attributes, such that Halodiplosis is limited to only 13 species developing in plant tissues without obvious gall formation or as inquilines in galls of other cecidomyiids. Revised status were proposed for Asiodiplosis, Onodiplosis, and Desertomyia, all species of which are gall inducers. A detailed morphological study of the Israeli species combined with data on their life history and an analysis of mitochondrial COI and 16S gene sequences revealed nine gall-inducing species belonging to Asiodiplosis and one inquilinous species belonging to Halodiplosis. All ten species (Asiodiplosis admirabilis n.sp., A. bimoda n.sp., A. delicatula n.sp., A. largifica n.sp., A. mohicana n.sp., A. mucronata n.sp., A. paradoxa n.sp., A. pillosaeconspicua n.sp., A. stellata n.sp., and Halodiplosis fugax n.sp.) are described here as new to science, including the first descriptions of larvae and pupae for these genera.

An Autochthonous Acidithiobacillus ferrooxidans Metapopulation Exploited for Two-Step Pyrite Biooxidation Improves Au/Ag Particle Release from Mining Waste

Pyrite bio-oxidation by chemolithotrophic acidophile bacteria has been applied in the mining industry to bioleach metals or to remove pyritic sulfur from coal. In this process, it is desirable to use autochthonous and already adapted bacteria isolated directly from the mining sites where biomining will be applied. Bacteria present in the remnant solution from a mining company were identified through cloning techniques. For that purpose, we extracted total RNA and performed reverse transcription using a novel pair of primers designed from a small region of the 16S gene (V1–V3) that contains the greatest intraspecies diversity. After cloning, a high proportion of individuals of the strains ATCC-23270 (NR_074193.1 and NR_041888.1) and DQ321746.1 of the well-known species Acidithiobacillus ferrooxidans were found, as well as two new wild strains of A. ferrooxidans. This result showed that the acidic remnant solution comprises a metapopulation. We assayed these strains to produce bioferric flocculant to enhance the subsequent pyrite bio-oxidation, applying two-stage chemical–bacterial oxidation. It was shown that the strains were already adapted to a high concentration of endogenous Fe2+ (up to 20 g·L−1), increasing the volumetric productivity of the bioferric flocculant. Thus, no preadaptation of the community was required. We detected Au and Ag particles originally occluded in the old pyritic flotation tailings assayed, but the extraction of Au and Ag by cyanidation resulted in ca. 30.5% Au and 57.9% Ag.

Molecular Diversity of Bacillus thuringiensis and Bioinformatics Analysis of Local Isolate of Auky Island, Padaido District in Biak Numfor Papua as a Control of Anopheles Mosquito Larvae

This research aims to analyze the level of similarity and diversity among local isolates of B. thuringiensis Auky Island Padaido District in Biak Numfor Regency with NCBI gene bank base, the basis of which is to obtain B. thuringiensis isolates from jayapura local isolates that can act as controllers of Anopheles mosquito larvae. Several steps in the research are 16s gene amplification, PCR product purification, cloning using pTA2 vectors and transformation into competent E. coli Zymo 5α cells, confirmation with PCR colonies, recombinant plasmid isolation, sequencing analysis and phylogenetic tree construction. The isolates of ABNP8, ABNP9, ABNP11, ABNP12 and ABNP18 have been detected as local isolates from in Auky Island Padaido District in Biak Numfor Papua Regency that have great potential as bioinsecticides, and capable of controlling and killing Anopheles mosquito larvae. Of the five isolates, ABNP8 isolates had unique diversity and characteristics and were different from the four other isolates. Based on the similarity analysis in the MEGA7 program, the similarity rate reached 84%. Its diversity can be seen from the uniqueness of the sequence and its position in different branching dendrograms.

Phylogeography of the Common New Zealand Wrasse Species, Notolabrus Celidotus, and the Phylogenetics of the Pseudolabrine Tribe

<p>The New Zealand coastline and marine environment is a diverse place and presents plenty of dispersal obstacles to many of the organisms that live there. This thesis investigates the phylogeography of one of the most common fish species around the coast of New Zealand, the endemic wrasse Notolabrus celidotus, using the mitochondrial DNA control region and compares genetic variability to another common New Zealand wrasse, Notolabrus fucicola in a local setting. These species are part of a tribe of temperate fish, the pseudolabrines, which can be found throughout the South and North-West Pacific. The phylogeny of this tribe was also analysed using the mitochondrial 16S gene to investigate the relationships among the New Zealand pseudolabrines and to those species elsewhere. The results suggest that pseudolabrines from mainland New Zealand are closely related and are likely to have originated from southern Australia while species from the Kermadec Islands and other northern islands are more closely related to the species of eastern Australia. The Notolabrus and Pseudolabrus genera should be reviewed to remedy paraphyly of Pseudolabrus. Furthermore, N. celidotus shows no population structuring throughout its range and appears to be rapidly expanding. Genetic variability was similar for both N. celidotus and N. fucicola. The results suggest that the pseudolabrine tribe has made multiple migrations to New Zealand where Notolabrus celidotus was able to spread around the three main islands and, likely facilitated by a long planktonic larval duration, was able to maintain high gene flow among populations.</p>

Phylogeography of the Common New Zealand Wrasse Species, Notolabrus Celidotus, and the Phylogenetics of the Pseudolabrine Tribe

<p>The New Zealand coastline and marine environment is a diverse place and presents plenty of dispersal obstacles to many of the organisms that live there. This thesis investigates the phylogeography of one of the most common fish species around the coast of New Zealand, the endemic wrasse Notolabrus celidotus, using the mitochondrial DNA control region and compares genetic variability to another common New Zealand wrasse, Notolabrus fucicola in a local setting. These species are part of a tribe of temperate fish, the pseudolabrines, which can be found throughout the South and North-West Pacific. The phylogeny of this tribe was also analysed using the mitochondrial 16S gene to investigate the relationships among the New Zealand pseudolabrines and to those species elsewhere. The results suggest that pseudolabrines from mainland New Zealand are closely related and are likely to have originated from southern Australia while species from the Kermadec Islands and other northern islands are more closely related to the species of eastern Australia. The Notolabrus and Pseudolabrus genera should be reviewed to remedy paraphyly of Pseudolabrus. Furthermore, N. celidotus shows no population structuring throughout its range and appears to be rapidly expanding. Genetic variability was similar for both N. celidotus and N. fucicola. The results suggest that the pseudolabrine tribe has made multiple migrations to New Zealand where Notolabrus celidotus was able to spread around the three main islands and, likely facilitated by a long planktonic larval duration, was able to maintain high gene flow among populations.</p>

Isolation and genomic amplification of fish and shrimps from mangrove ecosystems in North Sumatra

Mangrove is a very typical ecosystem with a high level of diversity of flora and fauna. However, mangrove ecosystems are also one of the most vulnerable locations to extinction due to the high disturbances that occur. Some of the species that are susceptible to such disturbances are fish and shrimp. The use of barcode DNA is considered a fairly effective way to evaluate the condition of fish and shrimp populations in North Sumatra. Therefore, this study aims to obtain information on the success of kit methods and amplification patterns of barcoding marks 16S for fish and shrimp in mangrove ecosystems North Sumatra. The results showed that the kit extraction method produced a pattern of band that varied thick, thin and even smear. PCR amplification results with the 16S gene showed a good band pattern and indicated that the 16S primer used can detect fish and shrimp species that are visualized in the form of DNA bands.

Molecular biology as a diagnostic tool for detection of Leptospira spp. in cows of a border region – case report

The reproductive efficiency of livestock is the basis for the success of livestock, dairy or beef, and having high reproductive performance depends on several factors within the production system and the presence of infectious diseases of the reproductive sphere in the herd is one of the factors that can compromise that efficiency. The aim of this study was to use molecular biology as a diagnostic tool for the detection of Leptospira spp. DNA in cows with reproductive disorders on a rural property in the municipality of Boca do Acre, Amazonas, Brazil. Vaginal mucus was collected from nine Nelore breeding cows with a history of abortion and birth of weak calves submitted to DNA extraction and nested-PCR technique for 16S gene amplification at the bacterial genus level. Of the nine samples analyzed, five (55.55%) amplified a product of 331bp. The municipality of Boca do Acre is bordered by Peru and Bolivia, and knowledge of the prevalence of the disease, serovars, and circulating Leptospira species is essential for the adoption of measures related to animal husbandry, as well as health education for ranchers and their workers to avoid a possible occupational infection since this disease is considered an important zoonosis. New molecular studies using primers that allow the identification of the Leptospira species and mainly pathogenic species should be conducted in this region in order to elucidate the possible species of this etiological agent and the possible reservoirs of the disease to begin the understanding of the epidemiology of this disease in cattle in this region of border.

Antisense noncoding mitochondrial RNA-2 gives rise to miR-4485-3p by Dicer processing in vitro

Background The antisense noncoding mitochondrial RNAs (ASncmtRNAs) derive from the mitochondrial 16S gene. Knockdown of these transcripts with chemically-modified antisense oligonucleotides induces proliferative arrest, apoptosis and invasiveness reduction in tumor but not normal cells. One of these transcripts, ASncmtRNA-2, contains the complete and identical sequence of hsa-miR-4485-3p and, upon knockdown of this transcript, there is a strong increase in levels of this miRNA, suggesting ASncmtRNA-2 as a source for miR-4485-3p, which is supported by several evidences from our group and others, in the ex vivo setting. Results Here we show that incubation of in vitro-transcribed ASncmtRNA-2 with recombinant Dicer produces RNA fragments corresponding to hsa-miR-4485-3p, showing that Dicer binds to and processes ASncmtRNA-2, strongly supporting the hypothesis that ASncmtRNA-2 acts as a precursor for miR-4485-3p. Conclusion The in vitro results presented here strengthen the hypothesis that miR-4485-3p is derived from ASncmtRNA-2 by Dicer processing. Since miR-4485-3p is classified as a tumor suppressor miRNA, this evidence strengthens the application of ASncmtRNA knockdown for cancer therapy.

Presence of distinctive microbiome in the first-pass meconium of newborn infants

We critically evaluated the fetal microbiome concept in 44 neonates with placenta, amniotic fluid, and first-pass meconium samples. Placental histology showed no signs of inflammation. Meconium samples were more often bacterial culture positive after vaginal delivery. In next-generation sequencing of the bacterial 16S gene, before and after removal of extracellular and PCR contaminant DNA, the median number of reads was low in placenta (48) and amniotic fluid (46) and high in meconium samples (14,556 C-section, 24,860 vaginal). In electron microscopy, meconium samples showed extracellular vesicles. Utilizing the analysis of composition of microbiomes (ANCOM) against water, meconium samples had a higher relative abundance of Firmicutes, Lactobacillus, Streptococcus, and Escherichia-Shigella. Our results did not support the existence of the placenta and amniotic fluid microbiota in healthy pregnancies. The first-pass meconium samples, formed in utero, appeared to harbor a microbiome that may be explained by perinatal colonization or intrauterine colonization via bacterial extracellular vesicles.