Purpose Truffles are colonized by a complex microbial community of bacteria, yeasts, and filamentous fungi, whose role has not yet been fully understood. The main purpose of the research was to characterize the bacterial communities associated with Tuber aestivum Vittad. fruiting bodies collected from natural truffle grounds in the Molise region (Southern Italy). Despite it is one of the Italian richest areas of truffles, little is known about truffles in Molise. Methods Six ripe fruiting bodies of Tuber aestivum Vittad. and six soil samples were collected in July 2018 at Villa San Michele in the municipality of Vastogirardi, Molise region. Then, soil and truffle microbial communities were analyzed through 16S rRNA gene sequencing on the Illumina MiSeq platform and bioinformatics analyses. Results Consistently with previous studies, the main phyla retrieved in the investigated ascocarps were Proteobacteria and Actinobacteria, with the genus Bradyrhizobium particularly represented. Nevertheless, significant differences between soil and truffle microbiota and an unexpected heterogeneity across truffles were observed. It is likely that a specific recruitment of bacteria from soil to ascocarps occurs during the truffle formation and that local-scale factors play an important role in determining the structure of the investigated truffle microbial communities. Conclusion Although further analyses (based on a larger soil and truffle sample size and aimed at defining in more detail microbial diversity, soil physical and chemical properties, microclimatic conditions, and vegetation) are required to better understand which are these factors and how they could influence the composition of truffle bacterial communities, this study represents the starting point for a deepened characterization of this economically important product.

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In the present study, the prokaryotic community structure of the water of Lake Balaton was investigated at the littoral region of three different points (Tihany, Balatonmáriafürdő and Keszthely) by cultivation independent methods [next-generation sequencing (NGS), specific PCRs and microscopy cell counting] to check the hidden microbial diversity of the lake. The taxon-specific PCRs did not show pathogenic bacteria but at Keszthely and Máriafürdő sites extended spectrum betalactamase-producing microorganisms could be detected. The bacterial as well as archaeal diversity of the water was high even when many taxa are still uncultivable. Based on NGS, the bacterial communities were dominated by Proteobacteria, Bacteroidetes and Actinobacteria, while the most frequent Archaea belonged to Woesearchaeia (Nanoarchaeota). The ratio of the detected taxa differed among the samples. Three different types of phototrophic groups appeared: Cyanobacteria (oxygenic phototrophic organisms), Chloroflexi (anaerobic, organotrophic bacteria) and the aerobic, anoxic photoheterotrophic group (AAPs). Members of Firmicutes appeared only with low abundance, and Enterobacteriales (order within Proteobacteria) were present also only in low numbers in all samples.

In the present study 12 water samples of five sampling sites (Tatabánya, Dandár, Szentendre, Szent Flórián and Ciprián groundwaters) known as nutrient-depleted aquatic environments were studied using amplicon sequencing (NGS) and cultivation techniques. Diversity indices and cell counts were determined to assess the species richness in relation to the cell counts within the samples, and the oligocarbophile growth capability of the isolated bacteria was tested in microtiter plates. Altogether, 55 bacterial phyla were identified from the samples by amplicon sequencing. The microbial communities of the different sampling times of the same sites did not differ significantly. Patescibacteria and Proteobacteria were present in all samples. Ciprián sample was dominated by Bacteroidetes, while in Dandár sample a high ratio of Chloroflexi was detected. Rokubacteria and WOR-1 dominated Szent Flórián sample and Tatabánya had a high number of Epsilonbacteraeota. Nine archaeal phyla were also detected; the samples were characterized by the presence of unclassified archaea and Nanoarchaeota, among them Woesearchaeia, as the most dominant. Crenarchaeota and Altiarchaeota were detected in high ratios in Dandár water samples. Among Thaumarchaeota the family Nitrosopumilaceae, and orders of Nitrosotaleales and Nitrososphaerales appeared in Szent Flórián and Tatabánya samples. Key organisms of the different biogeochemical cycles were discovered in these nutrient-depleted environments: methanogenic archaea, methanotrophic bacteria, ammonia oxidizer, nitrate reducers, diazotrophs, sulfate reducers, and sulfur oxidizer. Diversity indices and cell counts of the samples show negative correlation in case of bacteria and positive in case of archaea in Ciprián sample. The high diversity indices in Szentendre samples are connected to low cell counts, most probably due to the vulnerability of the groundwaters to the external environment factors which lead to the infiltration of soil microbes and contaminants to the water. The isolated bacteria were affiliated into four phyla, most of them belonging to Proteobacteria (59%) followed by Actinobacteria (21%), Firmicutes (17%) and Verrucomicrobia (1%). The members of the facultative chemolithotrophic genera of Sphingobium, Sphingomonas, Sphingopyxis were characterizing only Szentendre, Szent Flórián and Tatabánya samples. Only 10% of the isolated species showed an obligate oligocarbophile character. From the samples, a high number of novel bacterial taxa were cultivated. As a conclusion, our results confirmed the predominance of unclassified and unknown taxa in subsurface water, pointing to the importance and necessity of further studies to characterize these microbial populations.

The Moroccan coast is characterized by a diversity of climate, reflecting a great richness and diversity of fauna and flora. By this, marine microbiota plays a fundamental role in many biogeochemical processes, environmental modifications, and responses to temperature changes. To date, no exploration by high-throughput techniques has been carried out on the characterization of the Moroccan marine microbiota. The objective of this work is to study the diversity and metabolic functions of MMM from the Moroccan coast (Atlantic and Mediterranean) according to the water source (WS) and the type of climate (CT) using the approach high-throughput sequencing of the 16SrRNA gene. Four water samples of twelve sampling sites from the four major climates along the Moroccan coastline were collected, and prokaryotic DNA was extracted. V4 region of 16S rRNA gene was amplified, and the product PCR was sequenced by Illumina Miseq. The β-diversity and α-diversity indices were determined to assess the species richness and evenness. The obtained results were analyzed by Mothur and R software. A total of twenty-eight Bacterial phyla and twelve Archaea were identified from the samples. Proteobacteria, Bacteroidetes, and Cyanobacteria are the three key bacterial phyla, and the Archaeal phyla identified are: Euryarchaeota, Nanoarchaeaeota, Crenarchaeota, Hydrothermarchaeota, Asgardaeota, Diapherotrites, and Thaumarchaeota in the Moroccan coastline and the four climates studied. The whole phylum are involved in marine biogeochemical cycles, and through their functions they participate in the homeostasis of the ocean in the presence of pollutants or stressful biotic and abiotic factors. In conclusion, the obtained results reported sufficient deepness of sequencing to cover the majority of Archaeal and Bacterial genera in each site. We noticed a strong difference in microbiota diversity, abundance, and taxonomy inter- and intra-climates and water source without significant differences in function. To better explore this diversity, other omic approaches can be applied such as the metagenomic shotgun, and transcriptomic approaches allowing a better characterization of the Moroccan marine microbiota and to understand the mechanisms of its adaptation and its impacts in/on the ecosystem.

In the present study, water samples from 8 sites known as: Taploca, Nagy-borvíz, Piricske (located in Romania) and Szent Jakab, Kiskút, Kossuth Lajos, Polányi kút and Berzsenyi (located in Balaton highland in Hungary) and characterized with low nutrient content, were studied using cultivation independent methods. Diversity indices and cell counts were determined to assess the species richness in relation to the cell counts within the samples. Next generation sequencing was used to reveal the existing microbial community, and taxon specific PCR was used to detect the presence of some species with hygienic. 18 bacterial phyla above a ratio of 2% were identified in addition to 13 archaeal phyla using amplicon sequencing. Nagy-borvíz water sample showed a unique presence of Chloroflexi, Bacteroidota, Desulfobacterota, Acidobacteriota and Actinobacteriota. Piricske water sample showed mostly Caldisericota and Spirochaetota. Taploca water sample contained a unique presence of Planctomycetota and Myxococcota at the same time with Szent Jakab water sample which showed an additional presence of Chloroflexi, Berzsenyi contained Campylobacterota at the same time with Polányi kút which had important fractions of Nitrospirota and Desulfobacterota. Finally, Kossuth Lajos water sample was dominated by Fusobacteriota, mainly members of Hypnocyclicus genus. Piricske and especially Nagy-borvíz water samples contained important fractions of Altiarchaeota, moreover, Piricske contained high fraction of Euryarchaeota phylum -most of them belong to Methanobacteriaceae family. Nitrosopumilaceae dominated Taploca and Kiskút in addition to their important presence in the rest of the samples. Diversity indices and cell count showed in general that cell count values are tending to be lower when the diversity is higher. The results of taxon specific PCR reactions showed that water treatment would be essential in some water samples.

In the present study, water samples from 8 sites known as: Taploca, Nagy-borvíz, Piricske (located in Romania) and Szent Jakab, Kiskút, Kossuth Lajos, Polányi kút and Berzsenyi (located in Balaton highland in Hungary) and characterized with low nutrient content, were studied using cultivation independent methods. Diversity indices and cell counts were determined to assess the species richness in relation to the cell counts within the samples. Next generation sequencing was used to reveal the existing microbial community, and taxon specific PCR was used to detect the presence of some species with hygienic. 18 bacterial phyla above a ratio of 2% were identified in addition to 13 archaeal phyla using amplicon sequencing.Nagy-borvíz water sample showed a unique presence of Chloroflexi, Bacteroidota, Desulfobacterota, Acidobacteriota and Actinobacteriota. Piricske water sample showed mostly Caldisericota and Spirochaetota. Taploca water sample contained a unique presence of Planctomycetota and Myxococcota at the same time with Szent Jakab water sample which showed an additional presence of Chloroflexi, Berzsenyi contained Campylobacterota at the same time with Polányi kút which had important fractions of Nitrospirota and Desulfobacterota. Finally, Kossuth Lajos water sample was dominated by Fusobacteriota, mainly members of Hypnocyclicus genus.Piricske and especially Nagy-borvíz water samples contained important fractions of Altiarchaeota, moreover, Piricske contained high fraction of Euryarchaeota phylum -most of them belong to Methanobacteriaceae family.Nitrosopumilaceae dominated Taploca and Kiskút in addition to their important presence in the rest of the samples. Diversity indices and cell count showed in general that cell count values are tending to be lower when the diversity is higher. The results of taxon specific PCR reactions showed that water treatment would be essential in some water samples.

In Hungary, which is famous for its thermal baths, according to the regulations, waters are investigated in hygienic aspects with standard cultivation methods. In the present study, two thermal baths were investigated (the well and three different pool waters in both) using cultivation methods, taxon-specific polymerase chain reactions (PCRs), multiplex PCRs and next-generation amplicon sequencing. Mainly members of the natural microbial community of the well waters and bacteria originating from the environment were detected but several opportunistic pathogenic taxa, e.g., Pseudomonas aeruginosa, P. stutzeri, Acinetobacter johnsoni, Acinetobacter baumanni, Moraxella osloensis, Microbacterium paraoxydans, Legionella spp., Stenotrophomonas maltophilia and Staphylococcus aureus were revealed by the applied methods. Pools with charging-unloading operation had higher microscopic cell counts, colony-forming unit (CFU) counts, number of cocci, P. aeruginosa and S. aureus compared to the recirculation systems. Bacteria originating from human sources (e.g., skin) were identified in the pool waters with less than 1% relative abundance, and their presence was sporadic in the pools. Comparing the microbiological quality of the pools based on the first sampling time and the following four months' period it was revealed that recirculation operation type has better water quality than the charging-unloading pool operation from a hygienic point of view.