Seasonal dynamics of eukaryotic microbial diversity in hypersaline Tuz Lake characterized by 18S rDNA sequencing

Microbial diversity found in hypersaline ecosystems is structurally unique and essential in many microbiological and ecological processes. Tuz Lake, the second biggest lake in Türkiye, is a talassohaline (over 32% [w/v]) lake with near-neutral pH. The aim of study was to investigate the composition of the eukaryotic microbial community in Tuz Lake by 18S rDNA amplicon sequencing, as well as its relationship and change with environmental factors during 1-year period. Next-generation sequencing and bioinformatic analysis were applied to describe the eukaryotic microbial community in Tuz Lake. As a result of bioinformatics analysis, Archaeplastida (39%) and Stramenopiles, Alveolata, Rhizaria (SAR) (51%) were the most abundant taxa represented in the dataset. The Archaeplastida phylum showed a significant difference between winter and summer and higher abundance in summer in contrast to the SAR group, which represented higher abundance in winter. Genus level assessment showed that the most abundant genera were Navicula, Chlorophyta;unclassified_taxa, Dunaliella, Cladosporium, Paraphelidium, Scuticociliates;unclassified_taxa, and Chlamydomonadales;unclassified_taxa. Navicula abundance was significantly different and overwhelmingly dominant in winter. On the other hand, Cladosporium and Chlorophyta; unclassified_taxa represented a significant difference between seasons and high abundance in summer. Furthermore, Dunaliella populations were not detected in midsummer and early fall when the temperature increased and water volume in the lake decreased.

Prediction of minimum postmortem submersion interval (PMSImin) based on eukaryotic community succession on skeletal remains recovered from a lentic environment

Although recent studies explored using microbial succession during decomposition to estimate the postmortem interval (PMI) and postmortem submersion interval (PMSI), there is currently no published research using aquatic eukaryotic community succession to estimate the minimum postmortem submersion interval (PMSImin). The goals of this study were to determine whether eukaryotic community succession occurs on porcine skeletal remains in a lentic environment, and, if so, to develop a statistical model for PMSImin prediction. Fresh porcine bones (rib N = 100, scapula N = 100) were placed in cages (10'' x 10'') attached to floatation devices and submerged in a fresh water lake (Crozet, VA), using waterproof loggers and a YSI Sonde to record temperature and water quality variables, respectively. In addition to baseline samples, one cage, containing five ribs and five scapulae, and water samples (500 mL) were collected approximately every 250 accumulated degree days (ADD). Nineteen sample cohorts were collected over a period of 5200 ADD (579 Days). Variable region nine (V9) of the 18S ribosomal DNA (rDNA) was amplified and sequenced using a dual-index strategy on the MiSeq FGx sequencing platform. Resulting sequences underwent quality control parameters and analysis in mothur v 1.42.3, R v 3.5.3, and R v 3.6.0. Permutational multivariate analysis of variance (PERMANOVA) revealed a significant difference in phylogenetic β-diversity among ribs, scapulae and water (p = 0.001) and among ADD (p ≤ 0.011), which was supported by distinct clustering of samples associated with each ADD in UniFrac distance based non-metric multidimensional scaling (NMDS) ordinations. Using similarity percentage (SIMPER) analysis of class and family level taxa, differences observed between bone types were attributed to Peronosporomycetes_cl, Eukaryota_unclassified, and Intramacronucleata (e.g., Armophorida), however these differences were not statistically significant. Alpha diversity revealed a non-linear increase in phylogenetic diversity with an increase in ADD. Random forest models for ribs and scapulae predicted PMSImin with an error rate within±104 days (937 ADD) and±63 days (564 ADD), respectively. In conclusion, this study suggests that eukaryotic succession is capable of predicting long term PMSImin in lentic systems.

Altered fungal communities in contaminated soils from French industrial brownfields

Polycyclic aromatic hydrocarbons (PAHs) and metals are contaminants of industrial brownfield soils. Pollutants can have harmful effects on fungi, which are major actors of soil functioning. Our objective was to highlight fungal selection following long-term contamination of soils. Fungal diversity was assessed on 30 top-soil samples from ten sites gathered in three groups with different contamination levels and physico-chemical characteristics: 1) uncontaminated controls, 2) slag heaps displaying high PAH and moderate metal contaminations, and 3) settling ponds displaying high metal and intermediate PAH contaminations. Although fungal abundance and richness were similar among the soil groups, the diversity and evenness indices were lower for the slag heap group. Fungal diversity differed among soil groups at the phylum and OTU levels, and indicator species were identified. The relative abundance of Agaricomycetes, Saccharomycetes, Leotiomycetes and Chytridiomycota was higher in the control soils than in the two groups of contaminated soils. Cryptomycota LKM11 representatives were favoured in the slag heap and settling pond groups, and their relative abundance was correlated to the zinc and lead contamination levels. Dothideomycetes - positively linked to PAH contamination - and Eurotiomycetes were specific to the slag heap group. Pucciniomycetes and especially Gymnosporangium members were favoured in the settling pond soils.

Microbiological diagnosis of Acanthamoebic keratitis: experience from tertiary care center of North India

Acanthamoeba keratitis (AK) is a painful vision-threatening infection caused by pathogenic free-living Acanthamoeba. Due to the non-specific clinical presentation, this condition tends to be misdiagnosed by clinicians. A timely diagnosis is crucial for favorable visual outcome. Three hundred patients with suspected microbial keratitis presenting to the Advanced Eye Center at our tertiary care center in North India during the period from 2014 to 2018 were included. Patient's corneal scrapings, contact lens, lens solution, lens case, and tears were processed for microscopic examination by Giemsa and Calcofluor staining, non-nutrient agar (NNA) culture and molecular diagnosis by conventional PCR (cPCR) and Real-time PCR (qPCR). 18S rDNA gene sequencing was done to assess phylogenetic relationship. AK was found in 3.6% (11/300) of non-bacterial non-fungal keratitis patients. Among microbiological techniques, microscopy for Acanthamoeba was positive in 7 cases, NNA culture was positive in 9 cases and 11 cases were detected both by cPCR and qPCR. The sensitivity of microscopy, culture, cPCR and qPCR was 63.64%, 81.82 %, 100%, and 100% respectively whereas specificity was 100% for all the tests. 18S rDNA sequencing revealed that A. castellanii was the predominant species and isolates were genetically distinct. AK should be considered in the differential diagnosis of infectious keratitis. Molecular tests are useful for rapid, sensitive and specific diagnosis and must be included in workup of keratitis.

Structural variability and niche differentiation of the rhizosphere and endosphere fungal microbiome of Casuarina equisetifolia at different ages

BACKGROUND

Casuarina equisetifolia is one of the most important artificially planted protective forests along the coast in southern China for windbreaks, soil erosion, and sand dune stabilization. Self-renewing of C. equisetifolia is very limited, which might be caused by low soil nutrient levels and reduced microbial activity.

METHODS

Use of high-throughput sequencing of the 18S rDNA to investigate the microbial communities from the rhizosphere and root endosphere of C. equisetifolia in young-aged, intermediate-aged, and mature-aged forests.

RESULTS

Our results indicate that the diversity of rhizosphere fungal microbiomes in field-grown C. equisetifolia is much lower than that of the endosphere microbiomes. Bioinformatic analysis showed that rhizocompartments produce the strongest differentiation of rhizosphere and endosphere communities. Notably, the distribution of rhizosphere fungi communities was significantly influenced by the environmental factors, not by forest ages.

CONCLUSIONS

The presented study suggests that the rhizocompartments and environmental factors, rather than forest ages, determine the diversities of fungal community.

Taxonomy and 18S rDNA-based phylogeny of Henneguya multiradiatus n. sp. (Cnidaria: Myxobolidae) a parasite of Brochis multiradiatus from Peruvian Amazon

A new myxozoan species belonging to the genus Henneguya was isolated from the serous membrane of the visceral cavity of the hognosed catfish Brochis multiradiatus from Peruvian Amazon. Whitish plasmodia, macroscopically visible, were found in four of the thirty examined fishes. Mature myxospores were ellipsoidal in shape in frontal view and had a total length of 44.5 ± 0.6 μm (43.9-45.1), spore body measured 18.7 ± 0.9 μm (16.8-19.6) in length, 7.1 ± 0.2 μm (6.6-7.4) in width and 5.5 ± 0.3 μm (4.9-5.6) in thickness. The two polar capsules were elongated and equal in size, measuring 9.1 ± 0.1 μm (8.8-9.4) in length and 1.7 ± 0.1 μm (1.6-1.8) in width, occupying half of the myxospore body. Polar tubules coiled in 10-11 turns perpendicular to the long axis of the polar capsule. The caudal appendage was not bifurcated and measured 25.8 ± 0.6 μm (24.7-26.5) in length. The sequencing of the 18S rDNA gene resulted in 1400 bp and this sequence did not match any of the myxozoans available in GenBank. Phylogenetic analysis placed the new species in a well-supported subclade of Henneguya spp. infecting callichthyid fishes, with Henneguya loretoensis being the closest species. This study is the first description of a myxozoan species, Henneguya multiradiatus n. sp. from a fish of the genus Brochis.

Responses of Rhizosphere Fungal Communities to the Sewage Sludge Application into the Soil

Due to the increasing sewage sludge production in the world and problems with its disposal, an application of sludge to the soil appears to be a suitable solution considering its fertilizer properties and ability to improve the soil physical conditions. On the other hand, the sludge may also contain undesirable and toxic substances. Since soil microorganisms are sensitive to environmental changes, they can be used as indicators of soil quality. In this study, we used sewage sludge (SS) from two municipal wastewater treatment plants (SS-A and SS-B) in the dose of 5 t/ha and 15 t/ha in order to determine possible changes in the fungal community diversity, especially arbuscular mycorrhizal fungi (AMF), in the rhizosphere of Arundo donax L. Rhizosphere samples were collected in summer and autumn for two consecutive years and the fungal diversity was examined using terminal restriction fragment length polymorphism and 18S rDNA sequencing. Fungal alpha diversity was more affected by SS-A than SS-B probably due to the higher heavy metal content. However, based on principal component analysis and ANOSIM, significant changes in overall fungal diversity were not observed. Simultaneously, 18S rDNA sequencing showed that more various fungal taxa were detected in the sample with sewage sludge than in the control. Glomus sp. as a representative of AMF was the most represented. Moreover, Funneliformis in both samples and Rhizophagus in control with Septoglomus in the sludge sample were other representatives of AMF. Our results indicate that the short-term sewage sludge application into the soil does not cause a shift in the fungal community composition.

High protein- and high lipid-producing microalgae from northern australia as potential feedstock for animal feed and biodiesel

Microalgal biomass can be used for biodiesel, feed, and food production. Collection and identification of local microalgal strains in the Northern Territory, Australia was conducted to identify strains with high protein and lipid contents as potential feedstock for animal feed and biodiesel production, respectively. A total of 36 strains were isolated from 13 samples collected from a variety of freshwater locations, such as dams, ponds, and streams and subsequently classified by 18S rDNA sequencing. All of the strains were green microalgae and predominantly belong to Chlorella sp., Scenedesmus sp., Desmodesmus sp., Chlamydomonas sp., Pseudomuriella sp., Tetraedron caudatum, Graesiella emersonii, and Mychonastes timauensis. Among the fastest growing strains, Scenedesmus sp. NT1d possessed the highest content of protein; reaching up to 33% of its dry weight. In terms of lipid production, Chlorella sp. NT8a and Scenedesmus dimorphus NT8e produced the highest triglyceride contents of 116.9 and 99.13 μg mL(-1) culture, respectively, as measured by gas chromatography-mass spectroscopy of fatty acid methyl esters. These strains may present suitable candidates for biodiesel production after further optimization of culturing conditions, while their protein-rich biomass could be used for animal feed.