Bacterial diversity in vadose cave pools: evidence for isolated ecosystems

Microbial diversity of cave pools, especially vadose pools, has received relatively little attention. To help fill this gap, this study reports on the bacterial diversity of 17 pools in three New Mexican arid land caves: Carlsbad Cavern, Lechuguilla Cave, and Hell Below Cave. These pools are spread throughout the caves and, with two exceptions, are not connected. The pools share a basic water chemistry, with fresh water of the calcium-magnesium-bicarbonate type. These 17 pools have Chao1 values between 40 and 1738; the Shannon diversity averages 4.6 ± 1.1, ranging from 2.6 to 6.4; and the Simpson averages 0.881 ± 0.099, ranging from 0.622 to 0.981. No two pools had the same communities, even at the phylum level. Nitrospirae, Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria were found >5% abundance in nine or more cave pools. Actinobacteria, Chloroflexi, Fibrobacteres, Firmicutes and Plantomycetes were at >5 % in four to six pools. Of the top ten widespread bacterial genera, Nitrospira was found in all pools, with >5 % in eleven pools. Other common genera include Polyclorovans, Propionibacterium, Polaromonas, Haliangium, Bacillus, Subgroup 6 uncultured Acidobacteria, Candidatus Omnitrophica, and uncultured Nitrosomonadaceae. Presence of several potential nitrogen cycling bacteria (e.g., Nitrospira) in the study pools suggests that nitrogen cycling may be an important bacterial role. There is some evidence of human contamination, particularly in the heavily visited Big Room, Carlsbad Cavern, but it is not the dominant control. Rather than a single stable cave pool community, adapted to the cave pool ecosystem, the data show 17 different communities, despite relatively similar conditions. The data support the hypothesis that each pool is a unique, isolated ecosystem, with differences likely caused more by the isolation of each pool than by variable chemistry. Thus, the common habit of grouping samples, while useful for some questions, may not capture the diversity present in cave ecosystems.

Street food as potential sources of covid-19 disease propagation in central and West Africa: A short review

In December 2019, a local pneumonia outbreak of initially unknown cause was detected in Wuhan (Hubei, China) and was quickly determined to be caused by a novel coronavirus, named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This pandemic spread very quickly around the world and has begun its proliferation in Africa. Respect of hygienic rules is one of the best preventive methods. This study explored street ready to eat foods as potential vehicle of human contamination with SARSCoV-2. For this, a bibliographic search was carried out from March 15 to December 7, 2020. From the results, it is well known that the transmission of the coronavirus by direct digestive route is ruled out for now. However, some studies are trying to demonstrate gastrointestinal manifestations and potential fecal-oral transmission of the virus. So ready to eat foods such as fruits and vegetables, bread, chips, donut, gari, snacks, homemade yogurt, cake, fried yam, roasted products, kilichi, ... etc. should get particular attention due to potential risk of contamination by manipulators during conditioning and packaging, to prevent the proliferation of the virus. It then becomes urgent to engage the population’s attention concerning what and where they eat.

HuConTest: Testing human contamination in great ape samples

Modern human contamination is a common problem in ancient DNA studies. We provide evidence that this issue is also present in studies in great apes, which are our closest living relatives, for example in non-invasive samples. Here, we present a simple method to detect human contamination in short read sequencing data from different species. We demonstrate its feasibility using blood and tissue samples from these species. This test is particularly useful for more complex samples (such as museum and non-invasive samples) which have smaller amounts of endogenous DNA, as we show here.

Microbial Community Structure Driven by a Volcanic Gradient in Glaciers of the Antarctic Archipelago South Shetland

It has been demonstrated that the englacial ecosystem in volcanic environments is inhabited by active bacteria. To know whether this result could be extrapolated to other Antarctic glaciers and to study the populations of microeukaryotes in addition to those of bacteria, a study was performed using ice samples from eight glaciers in the South Shetland archipelago. The identification of microbial communities of bacteria and microeukaryotes using 16S rRNA and 18S rRNA high throughput sequencing showed a great diversity when compared with microbiomes of other Antarctic glaciers or frozen deserts. Even the composition of the microbial communities identified in the glaciers from the same island was different, which may be due to the isolation of microbial clusters within the ice. A gradient in the abundance and diversity of the microbial communities from the volcano (west to the east) was observed. Additionally, a significant correlation was found between the chemical conditions of the ice samples and the composition of the prokaryotic populations inhabiting them along the volcanic gradient. The bacteria that participate in the sulfur cycle were those that best fit this trend. Furthermore, on the eastern island, a clear influence of human contamination was observed on the glacier microbiome.

Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets

Background After over a decade of developments in field collection, laboratory methods and advances in high-throughput sequencing, contamination remains a key issue in ancient DNA research. Currently, human and microbial contaminant DNA still impose challenges on cost-effective sequencing and accurate interpretation of ancient DNA data. Results Here we investigate whether human contaminating DNA can be found in ancient faunal sequencing datasets. We identify variable levels of human contamination, which persists even after the sequence reads have been mapped to the faunal reference genomes. This contamination has the potential to affect a range of downstream analyses. Conclusions We propose a fast and simple method, based on competitive mapping, which allows identifying and removing human contamination from ancient faunal DNA datasets with limited losses of true ancient data. This method could represent an important tool for the ancient DNA field.

Competitive mapping allows to identify and exclude human DNA contamination in ancient faunal genomic datasets

BackgroundAfter over a decade of developments in field collection, laboratory methods and advances in high-throughput sequencing, contamination remains a key issue in ancient DNA research. Currently, human and microbial contaminant DNA still impose challenges on cost-effective sequencing and accurate interpretation of ancient DNA data.ResultsHere we investigate whether human contaminating DNA can be found in ancient faunal sequencing datasets. We identify variable levels of human contamination, which persists even after the sequence reads have been mapped to the faunal reference genomes. This contamination has the potential to affect a range of downstream analyses.ConclusionsWe propose a fast and simple method, based on competitive mapping, which allows identifying and removing human contamination from ancient faunal DNA datasets with limited losses of true ancient data. This method could represent an important tool for the ancient DNA field.

Pathogenic Leptospira in Commensal Small Mammals from the Extensively Urbanized Coastal Benin

Leptospirosis is caused by spirochete bacteria of the genus Leptospira that affect one million and kill 60,000 persons annually in the world, who get infected through environmental mammal-excreted (notably rodent) pathogens. Using qPCR and DNA sequencing approaches, we here examine Leptospira occurrence and diversity in 971 commensal small mammals in urban and peri-urban habitats from south Benin, where socio-environmental conditions are favorable for human contamination. Prevalence reached 12.9% on average, but showed very important variations in both space and time, thus pointing toward a role of local processes in the maintenance and circulation of rodent-borne leptospires in the area. Prevalence peaks may occur during or one month after moderate (100–200 mm) monthly rainfall, suggesting that rodent-borne leptospires may be more prevalent when standing waters are present, but not at their highest levels (i.e., floods). However, this pattern will have to be confirmed through proper diachronic analysis. Finally, an incomplete but significant host-specificity was observed, with L. kirschneri retrieved only in African shrews, and the invasive Rattus norvegicus and the native Mastomys natalensis preferentially infected by L. interrogans and L. borgpeterseni, respectively. Our study highlights the urgent need for investigations on human leptospirosis in the extensively urbanized Abidjan–Lagos corridor.