Pyrosequencing analysis of fungal assemblages from geographically distant, disparate soils reveals spatial patterning and a core mycobiome

Identifying a soil core microbiome is crucial to appreciate the established microbial consortium, which is not usually subjected to change and, hence, possibly resistant/resilient to disturbances and a varying soil context. Fungi are a major part of soil biodiversity, yet the mechanisms driving their large-scale ecological ranges and distribution are poorly understood. The degree of fungal community overlap among 16 soil samples from distinct ecosystems and distant geographic localities (truffle grounds, a Mediterranean agro-silvo-pastoral system, serpentine substrates and a contaminated industrial area) was assessed by examining the distribution of fungal ITS1 and ITS2 sequences in a dataset of 454 libraries. ITS1 and ITS2 sequences were assigned to 1,660 and 1,393 Operational Taxonomic Units (OTUs; as defined by 97% sequence similarity), respectively. Fungal beta-diversity was found to be spatially autocorrelated. At the level of individual OTUs, eight ITS1 and seven ITS2 OTUs were found in all soil sample groups. These ubiquitous taxa comprised generalist fungi with oligotrophic and chitinolytic abilities, suggesting that a stable core of fungi across the complex soil fungal assemblages is either endowed with the capacity of sustained development in the nutrient-poor soil conditions or with the ability to exploit organic resources (such as chitin) universally distributed in soils

Lichens as natural sources of biotechnologically relevant bacteria

International audienceThe search for microorganisms from novel sources and in particular microbial symbioses represents a promising approach in biotechnology. In this context, lichens have increasingly become a subject of research in microbial biotechnology, particularly after the recognition that a diverse community of bacteria other than cyanobacteria is an additional partner to the traditionally recognized algae-fungus mutualism. Here, we review recent studies using culture-dependent as well as culture-independent approaches showing that lichens can harbor diverse bacterial families known for the production of compounds of biotechnological interest and that several microorganisms isolated from lichens, in particular Actinobacteria and Cyanobacteria, can produce a number of bioactive compounds, many of them with biotechnological potential

Enhanced phylogenetic analysis and targeted search for the genus Kribbella

[Not OCR'd

Cyanobacteria

Cyanobacteria are oxygenic organisms that play crucial roles in the cycles of carbon, nitrogen, and oxygen. They are ideal model organisms for studying photosynthesis, nitrogen fixation, and other biological processes. In addition, cyanobacteria are well recognized for their potential for a variety of biotechnological applications. This book presents a comprehensive overview of this interesting and useful group of bacteria. Chapters discuss such topics as the molecular methods applied for identifying freshwater toxigenic cyanobacteria, the diverse industrial applications of cyanobacteria, the potential of cyanobacteria in wound healing, the production of a novel hemoglobin by Synechocystis sp. PCC 6803, and the diversity, distribution, and applications of cyanobacteria in the Brazilian coastline

Revealing the dissimilar structure of microbial communities in different WWTPs that treat fish-canning wastewater with different NaCl content

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. This research was supported by the Spanish Government (Spanish Ministry of Science and Innovation) through TREASURE-TECHNOSALT (CTQ2017-83225-C2-1-R) and TREASURE-MICROSALT (CTQ2017-83225-C2-2-R) projects. The authors Alba Roibas-Rozas and Anuska Mosquera-Corral belong to the Galician Competitive Research Group GRC-ED431C 2017-29 and to the CRETUS Strategic Partnership (ED431E 2018/01) . All these programmes are co-funded by FEDER (UE) . Funding for open access charge: Universidad de Granada/CBUA.Studies that characterize the microbial communities in wastewater treatment plants (WWTPs) are numerous, yet similar studies in industrial WWTPs treating fish-canning effluents are limited. The microbial communities in samples of 4 fish-canning WWTPs that operated under different NaCl concentrations were investigated by qPCR and partial 16S rRNA gene Illumina sequencing. The absolute abundances of key microbial populations (Total Bacteria, Archaea and Fungi, ammonium oxidizing bacteria (AOB), Mycolata, Candidatus Microthrix, Ca. Accumulibacter and Ca. Competibacter) presented statistical differences among the WWTPs. The NaCl concentration negatively affected the absolute abundance of Bacteria and Fungi, filamentous, and phosphate (PAO) and glycogen (GAO) accumulating bacteria, while AOB and Ca. Microthrix populations were statistically higher in the WWTP with higher NaCl contents. On the other hand, the main bacterial operational taxonomic units (OTUs) were classified as members of Kouleothrix (Chloroflexia, Chloroflexi) and Tetrasphaera (Actinomycetia, Actinobacteria), family Beijerinckiaceae (Alphaproteobacteria, Proteobacteria), order Betaproteobacteriales (Gammaproteobacteria, Proteobacteria), Sphingobacteriales (Sphingobacteriia, Bacteroidetes) and Frankiales (Actinobacteria, Actinobacteria), class Anaerolineae (Chloroflexi), phylum Chloroflexi and Bacteria_unclassified. The structure of the bacterial community was highly dissimilar among the 4 WWTPs, as the identities of the dominant OTUs differed significantly among them. Therefore, the individual characteristics of the different WWTPs, mainly NaCl concentration, were responsible for the narrow assemblage of the bacterial communities. Different OTUs belonging to the phyla Actinobacteria, Bacteroidetes, Chloroflexi, Gemmatimonadetes and Proteobacteria were revealed as salttolerant. Taking into account these results, NaCl content was an important driver of the abundance of microbial populations and the bacterial community structure in the analysed industrial facilities.Spanish Government (Spanish Ministry of Science and Innovation) CTQ2017-83225-C2-1-R CTQ2017-83225-C2-2-REuropean CommissionGalician Competitive Research Group GRC-ED431C 2017-29CRETUS Strategic Partnership ED431E 2018/0

Characterization of Aspergillus species on Brazil nut from the Brazilian Amazonian region and development of a PCR assay for identification at the genus level.

Brazil nut is a protein-rich extractivist tree crop in the Amazon region. Fungal contamination of shells and kernel material frequently includes the presence of aflatoxigenic Aspergillus species from the section Flavi. Aflatoxins are polyketide secondary metabolites, which are hepatotoxic carcinogens in mammals. The objectives of this study were to identify Aspergillus species occurring on Brazil nut grown in different states in the Brazilian Amazon region and develop a specific PCR method for collective identification of member species of the genus Aspergillus. Results:Polyphasic identification of 137 Aspergillus strains isolated from Brazil nut shell material from cooperatives across the Brazilian Amazon states of Acre, Amapá and Amazonas revealed five species, with Aspergillus section Flavi species A. nomius and A. flavus the most abundant. PCR primers ASP_GEN_MTSSU_F1 and ASP_GEN_MTSSU_R1 were designed for the genus Aspergillus, targeting a portion of the mitochondrial small subunit ribosomal RNA gene. Primer specificity was validated through both electronic PCR against target gene sequences at Genbank and in PCR reactions against DNA from Aspergillus species and other fungal genera common on Brazil nut. Collective differentiation of the observed section Flavi species A. flavus, A. nomius and A. tamarii from other Aspergillus species was possible on the basis of RFLP polymorphism. Conclusions:Given the abundance of Aspergillus section Flavi species A. nomius and A. flavus observed on Brazil nut, and associated risk of mycotoxin accumulation, simple identification methods for such mycotoxigenic species are of importance for Hazard Analysis Critical Control Point system implementation. The assay for the genus Aspergillus represents progress towards specific PCR identification and detection of mycotoxigenic species

Biological basis of water quality assessment : the Kavango river, Namibia

Le fleuve Kavango prend sa source dnas les hauts plateaux d'Angola, se dirige vers le sud formant la frontière Angola-Namibie sur 415 km de direction Ouest-Est, et coule ensuite vers le sud pendant 65 km avant de former le delta de l'Okavango au Botswana. La portion moyenne de la rivière le long de la frontière est caractéristique des fleuves de faible pente des plaines d'inondation. Les crues sont d'environ 6 m au-dessus du niveau normal, avec un lit majeur de 5 km de large. Le fleuve est vital pour les populations locales dont 85% vivent à moins de 10 km du fleuve. Compte tenu des prévisions d'accroissement de la population, des besoins en eau, des programmes de redistribution des terres, de l'évolution des pratiques agricoles et d'une sécheresse chronique, le ministère des Pêches et des Ressources marines prépare les bases d'une gestion durable des ressources dont les populations locales sont directement dépendantes. C'est dans ce cadre qu'une recherche a été mise en place pour définir un protocole de suivi de la qualité des eaux en Namibie, protocole basé sur des critères biologiques. L'utilisation de critères biologiques pour suivre la qualité des cours des rivières dans les pays tempérés est commune. C'est moins le cas pour les pays tropicaux. L'indice d'intégrité biologique (IBI) est utilisé depuis plus de 10 ans en Europe et en Amérique du Nord. Il permet une estimation de la santé d'une rivière par l'analyse de son peuplement de poissons. Des données sur le peuplement de la portion namibienne du Kavango, obtenues en 1992, sont utilisées ici pour base d'un indice approprié. Les limites de l'approche sont analysées et des recommandations pour son extension à d'autres pays au sud du Sahara sont présentés. (Résumé d'auteur

Endophytic microorganisms of tropical tuber crops: Potential and perspectives

Endophytic microorganisms which include both bacteria and fungi colonise almost every plant species. In order to colonize the plant and compete with other microorganisms, they produce a plethora of secondary metabolites, including toxins, enzymes, antibiotics, anti-cancer, anti-inflammatory and antifungal compounds. Endophytic fungi can have profound impacts on plant communities which include abiotic and biotic stress tolerance, increase of biomass, decrease of water consumption and alteration of resource allocation, nitrogen fixation, increased drought resistance, thermal protection, survival under osmotic stress and degradation of pollutants. Though tuber crops are the second most important group of crop plants providing food energy to humans after cereals, less attention has been paid to the these traditional crops in general. Investigations regarding the association of endophytes with the tuber crops have been sparsely studied though in some tuber crops like cassava, sweet potato and yams, presence of endophytes have been reported. Hence from the scarcely available literature, in the current review an attempt was made to put light on the various beneficial activities of endophytes on tuber crops. These reports glorified many symbiotically associated endophytes to have antagonistic properties against many plant pathogens like Rhizoctoniasolani, Pythiumaphanidermatumand Sclerotiumrolfsii. Species like Rahnellawas resilient to cold shock, UV irradiation and antibiotics. Many diazotropihic and non-diazotropihicendophytic bacteria were involved in nitrogen fixation. Actinomycetesendophytes were novel sources of industrially important thermostableamylolytic enzymes. However, inspite of all these profound beneficial effects endophytic associations are still to be studied in many tuber crops like taro, elephant foot yam, greater yam etc. So this review put forward the urge to carry out comprehensive research on these important microbes on such important crops