Aquisphaera insulae sp. nov., a new member in the family Isosphaeraceae, isolated from the floating island of Loktak lake and emended description of the genus Aquisphaera

Bioaugmented biological contact oxidation reactor for treating simulated textile dyeing wastewater

In this study, modified polyamide fibers were used as biocarriers to enrich dense biofilms in a multi-stage biological contact oxidation reactor (MBCOR) in which partitioned wastewater treatment zone (WTZ) and bioaugmentation zone (BAZ) were established to enhance the removal of methyl orange (MO) and its metabolites while minimizing sludge yields. WTZ exhibited high biomass loading capacity (5.75 ± 0.31 g/g filler), achieving MO removal rate ranging from 68 % to 86 % under different aeration condition within 8 h in which the most dominant genus Chlorobium played an important role. In the BAZ, Pseudoxanthomonas was the dominant genus while carbon starvation stimulated the enrichment of chemoheterotrophy and aerobic_chemoheterotrophy genes thereby enhanced the microbial utilization of cell-released substrates, MO as well as its metabolic intermediates. These results revealed the mechanism bioaugmentation on MBCOR in effectively eliminating both MO and its metabolites.

Fungal and bacterial communities and their associations in snow-free and snow covered (sub-)alpine Pinus cembra forest soils

BACKGROUND

In Europe, Pinus cembra forests cover subalpine and alpine areas and they are of high conservational and ecological relevance. These forests experience strong seasonality with alternating snow-free and snow covered periods. Although P. cembra is known for mycorrhization and mycorrhizae usually involve fungi, plants and bacteria, the community compositions of fungi and bacteria and their associations in (sub-)alpine P. cembra forests remain vastly understudied. Here, we studied the fungal and bacterial community compositions in three independent (sub-)alpine P. cembra forests and inferred their microbial associations using marker gene sequencing and network analysis. We asked about the effect of snow cover on microbial compositions and associations. In addition, we propose inferring microbial associations across a range of filtering criteria, based on which we infer well justified, concrete microbial associations with high potential for ecological relevance that are typical for P. cembra forests and depending on snow cover.

RESULTS

The overall fungal and bacterial community structure was comparable with regards to both forest locations and snow cover. However, occurrence, abundance, and diversity patterns of several microbial taxa typical for P. cembra forests differed among snow-free and snow covered soils, e.g. Russula, Tetracladium and Phenoliphera. Moreover, network properties and microbial associations were influenced by snow cover. Here, we present concrete microbial associations on genus and species level that were repeatedly found across microbial networks, thereby confirming their ecological relevance. Most importantly, ectomycorrhizal fungi, such as Basidioascus, Pseudotomentella and Rhizopogon, as well as saprobic Mortierella changed their bacterial association partners depending on snow cover.

CONCLUSION

This is the first study researching fungal-bacterial associations across several (sub-)alpine P. cembra forests. The poorly investigated influence of snow cover on soil fungi and bacteria, especially those mycorrhizing P. cembra roots, but also saprobic soil organisms, underlines the relevance of forest seasonality. Our findings highlight that the seasonal impact of snow cover has significant consequences for the ecology of the ecosystem, particularly in relation to mycorrhization and nutrient cycling. It is imperative to consider such effects for a comprehensive understanding of the functioning resilience and responsiveness of an ecosystem.

Uncovering the biotechnological capacity of marine and brackish water Planctomycetota

An appealing strategy for finding novel bioactive molecules in Nature consists in exploring underrepresented and -studied microorganisms. Here, we investigated the antimicrobial and tumoral anti-proliferative bioactivities of twenty-three marine and estuarine bacteria of the fascinating phylum Planctomycetota. This was achieved through extraction of compounds produced by the Planctomycetota cultured in oligotrophic medium followed by an antimicrobial screening against ten relevant human pathogens including Gram-positive and Gram-negative bacteria, and fungi. Cytotoxic effects of the extracts were also evaluated against five tumoral cell lines. Moderate to potent activities were obtained against Enterococcus faecalis, methicillin-sensitive and methicillin-resistant Staphylococcus aureus and vancomycin-sensitive and vancomycin-resistant Enterococcus faecium. Anti-fungal effects were observed against Trichophyton rubrum, Candida albicans and Aspergillus fumigatus. The highest cytotoxic effects were observed against human breast, pancreas and melanoma tumoral cell lines. Novipirellula caenicola and Rhodopirellula spp. strains displayed the widest spectrum of bioactivities while Rubinisphaera margarita ICM_H10T affected all Gram-positive bacteria tested. LC-HRMS analysis of the extracts did not reveal the presence of any known bioactive natural product, suggesting that the observed activities are most likely caused by novel molecules, that need identification. In summary, we expanded the scope of planctomycetal species investigated for bioactivities and demonstrated that various strains are promising sources of novel bioactive compounds, which reenforces the potential biotechnological prospects offered by Planctomycetota.

Gemmata algarum, a Novel Planctomycete Isolated from an Algal Mat, Displays Antimicrobial Activity

Axenic cultures of two strains, JC673T and JC717, both belonging to the phylum Planctomycetota, were isolated from distinct geographical locations in India. Strain JC673T was obtained from algal mats of a wetland situated in the state of Kerala, India, while strain JC717 originated from the Central Marine Fisheries Research Institute (CMFRI), state of Tamil Nadu, India. The two strains share 99.9% 16S rRNA gene sequence similarity and are most closely related to Gemmata obscuriglobus UQM 2246T (99.3% 16S rRNA gene sequence identity). The newly isolated strains are Gram-negative, grow aerobically and tolerate up to 4% (w/v) NaCl and a pH of up to 9.0. Cells are spherical and form pink-pigmented colonies. The respiratory quinone is MK-6. Major fatty acids are C18:0, C16:1ω5c and C16:0. Polar lipids include phosphatidylcholine, phosphatidylethanolamine, several unidentified amino lipids, unidentified phospholipids, additional unidentified lipids, and an unidentified choline lipid. The polyamine spermidine is produced by the two strains. The strains have a genome size of about 8.2 Mb with a DNA G+C content of 67.6%. Solvent-based culture extracts of the isolates showed antimicrobial activity against three bacterial test strains. Their phylogenetic position along with differences in morphological, physiological, and genomic features support the classification as a new species of the genus Gemmata, for which we propose the name Gemmata algarum sp. nov. Strain JC673T (=KCTC 72851T = NBRC 114340T) and JC717 are the type and non-type strain of the new species, respectively.

Microbial features of mature and abandoned soils in refractory clay deposits

Processes of soil restoration in anthropogenically disturbed soils is an urgent topic in modern ecology and nature management. Being mediator between mineral soil composition and plant vegetation, soil microbial community is important factor of soil restoration processes. Analysis of main soil nutrition components followed by 16S amplicon sequencing are sufficient methods for primary analysis of novel locations. Here is the primary analysis in a novel location in Northwest Europe (Russia). Main nutrition parameters (pH, P, Na and NH₄⁺) and 16S rDNA Illumina amplicons were explored in abandoned soils from sandy pit quarry (2 sites) and refractory clay mining dumps (4 sites).Microbial communities of mature soils and dumps are variable and different in terms both nutritional and microbial components. pH, N and TOC are strong predictors for microbial composition. Dumps of refractory clays pQ_2 are non-developed soils, highly acidic and form specific microbial community. Differences between dumps and mature soils in both pre-quaternary and quaternary soils are connected with specific bacterial taxa. Those taxa are connected more with plant composition, not the soil properties themselves. The exact changes in microbial community are unique for different soils and areas.

Bacterial diversity of a floating vegetation (Phumdi) of Loktak Lake and its extracellular enzymes and bacterial antagonistic property

134 bacterial strains were isolated from phumdis of Loktak Lake. Through 16S rRNA sequencing, Bacillus sp. (23, 17.1%), Staphylococcus sp. (14, 10.4%), Pseudomonas sp. (11, 8.2%) and Acinetobacter sp. (8, 5.9%) were identified as the predominant bacterial taxa of Loktak Lake. B. pumulis (12, 8.9%), S. arlettae (4, 2.9%), P. knackmussii (6, 4.4%) are the leading species of Bacillus, Staphylococcus and Pseudomonas, respectively. Similarly, A. seifertii (2, 1.4%) and A. calcoaceticus (2, 1.4%) are the common species of Acinetobacter. 75 (55.9%) bacterial strains showed the ability to hydrolyze one or more extracellular enzymes tested. Among the extracellular enzymes produced by the bacterial isolates, the presence of elastase activity cannot be underestimated, since the enzyme is involved in the process of bacterial lung infection. Phosphate solubilizing activity could be seen in 11.1% of the bacterial isolates. 27 (20.1%) of the strains shown to have antagonistic activity against one or more tested pathogens. An isolate, MRC 52 showed antagonistic activity against eleven different pathogens including carbapenem resistant E. coli which was further subjected to extraction and identification of the biomolecule exerting the antimicrobial property. Based on GC-MS analysis, the bioactive compound was identified as phenyl ethyl alcohol.

Rubinisphaera margarita sp. nov., a novel planctomycete isolated from marine sediments collected in the Portuguese north coast

The phylum Planctomycetota is constituted by bacteria with unique features that are well adapted to a vast range of habitats. Here, we describe a novel planctomycete isolated from marine sediments collected on a beach in Matosinhos (Portugal) using an iChip-based culturing technique. Strain ICM_H10T forms beige-coloured colonies in modified M14 medium and its cells are spherical to ovoid in shape, stalked, rosette-forming and showing motility in a phase of the life cycle. Transmission electron microscopy observations showed a typical planctomycetal cell plan and cell division by budding. This strain requires salt for growth and grows in the range of 2.0–5.0 % (w/v) NaCl, from 20 to 37 °C, within a pH of 6.0–9.0 and is able to use diverse nitrogen and carbon sources. It is heterotrophic, aerobic and capable of microaerobic growth. This strain has a genome size of approximately 6.0 Mb and a G+C content of 58.1 mol%. A 16S rRNA gene-based phylogenetic analysis supports the association of strain ICM_H10T to the phylum Planctomycetota and the family Planctomycetaceae , as it shares only 96.8 and 96.4% similarity to its closest relatives Rubinisphaera italica Pan54T and Rubinisphaera brasiliensis IFAM 1448T, respectively. Other phylogenetic markers also support the separation of this strain into a novel species. Morphological, physiological and genomic comparisons between strain ICM_H10T and its closest relatives strongly suggest that ICM_H10T represents a new species of the genus Rubinisphaera , for which we propose the name Rubinisphaera margarita sp. nov., with ICM_H10T (=CECT 30326T=LMG 32234T) as type strain.

The Planctomycetia: an overview of the currently largest class within the phylum Planctomycetes

The phylum Planctomycetes comprises bacteria with uncommon features among prokaryotes, such as cell division by budding, absence of the bacterial tubulin-homolog cell division protein FtsZ and complex cell plans with invaginations of the cytoplasmic membrane. Although planctomycetes are ubiquitous, the number of described species and isolated strains available as axenic cultures is still low compared to the diversity observed in metagenomes or environmental studies. An increasing interest in planctomycetes is reflected by the recent description of a large number of new species and their increasing accessibility in terms of pure cultures. In this review, data from all taxonomically described species belonging to Planctomycetia, the class with the currently highest number of characterized members within the phylum Planctomycetes, is summarized. Phylogeny, morphology, physiology, ecology and genomic traits of its members are discussed. This comprehensive overview will help to acknowledge several aspects of the biology of these fascinating bacteria.

Aquisphaera insulae sp. nov., a new member in the family Isosphaeraceae, isolated from the floating island of Loktak lake and emended description of the genus Aquisphaera

Strain JC669^T was isolated from a floating island of Loktak lake, Manipur, India and shares the highest 16S rRNA gene sequence identity with Aquisphaera giovannonii OJF2^T. The novel strain is aerobic, Gram negative, light pink-coloured, non-motile, NaCl intolerant and spherical to oval-shaped. It grows in the form of single cells or aggregates and possibly forms structures which appear like fruiting bodies. Strain JC669^T grows well up to pH 9.0.The isolate produces MK-6 as respiratory quinone, C_18:1ω9c, C_16:0 and C_18:0 as major fatty acids and phosphatidylcholine, an unidentified amino lipid, an unidentified choline lipid (UCL) and six additional unidentified lipids (UL1, 2, 3, 4, 5, 6) as polar lipids. Strain JC669^T has a large genome size of 10.04 Mb and the genomic G + C content was 68.5 mol%. The genome contained all genes essential for lycopene related carotenoid biosynthesis. The polyphasic analysis of its phylogenetic position, morphological, physiological and genomic features supports the classification of strain JC669^T as a novel species of the genus Aquisphaera, for which we propose the name Aquisphaera insulae sp. nov. Strain JC669^T (= KCTC 72672^T = NBRC 114306^T) is the type strain of the novel species.