ITS rRNA Gene Research Articles

Diversity characterization of bacteria and fungi in water, sediments and biofilms from Songhua River in Northeast China

Water, sediments, and biofilms are the typical microbial carriers in natural water environments. However, comparative analysis of the distribution of bacterial and fungal communities in different carriers within the same habitat is relatively lacking. Therefore, this study employed 16 S and ITS rRNA gene sequencing to identify bacterial and fungal community structures in water, sediments, and biofilm. The results show that (1) the OTUs numbers revealed that the bacterial abundance, at the levels of species, genus, and family, followed the order of sediments > water > biofilms, while the fungal abundance order was water > sediments > biofilms. In addition, bacteria were mainly present in sediments, while fungi were mainly present in water. (2) The α diversity index (Shannon, ACE, Simpson, and Chao1) order, for bacteria was: sediments > water > biofilms, indicating that the diversity and homogeneity of bacteria in sediments were relatively higher; for fungi was: water > sediments > biofilms, indicating that the diversity and abundance of fungi in water were high. (3) The core phylum of bacterial in the water, sediments, and biofilms was Cyanobacteria (31.3–46.1%) and Actinobacteria (27.6–36.1%); Proteobacteria (35.0–41.8%), Cyanobacteria (14.7–36.6%); and Proteobacteria (63.3–69.2%), respectively. (4) The mainly colonized fungal phyla in biofilms in the water, sediments, and biofilms were Basidiomycota (29.3–38.7%) and Ascomycota (16.2–27.7%); Zygomycota (13.1–17.5%), Basidiomycota (5.6–17.6%); and Zygomycota (23.8–44.2%). (5) There were significant species differences in bacterial and fungal communities in water, sediments, and biofilm by NMDS analysis. Findings are useful for guiding significance for the Biogeochemical cycle of elements, the environmental fate of pollutants, and the study of water ecosystems.

Molecular analysis separates the Atlantic population of Montagu's stellate barnacle into two cryptic species

AbstractThe distribution of the intertidal barnacle Chthamalus montagui spans the West Mediterranean Sea and the Northeast Atlantic shores of Europe and West Africa. Knowledge of the phylogeography of this species has been limited to the Mediterranean and the European shores of the Atlantic. The present study considers the populations of West Europe, but also focuses on the overlooked populations of West Africa. We performed a molecular analysis using two markers: the mitochondrial COI gene and the nuclear rRNA ITS gene. Whereas ITS proved to be non‐informative, COI has demonstrated that the East Atlantic population of C. montagui comprises two genetically distinct clades: a northern clade that ranges from Mauritania to Scotland and a southern clade that comprises the populations from Senegal. These clades are separated by the Cape Verde Front, which stretches west of the upwelling area off Mauritania. We consider these clades as two cryptic species of the nominal species C. montagui.

Land utilization types impacted the species diversity and population distribution of nodulating and non-nodulating rhizobia in the Philippines

The influence of three land utilization types (LUT) on the diversity and population of soybean-nodulating rhizobia indicated how human activities affect the ecology of these microorganisms. This report revealed that based on LUT (LUT1-rice-based; LUT2-soybean-based; LUT3-legume-rice), different species of rhizobia can be more abundant than the other species. Targeting the 16S rRNA gene and the 16S-23S rRNA gene ITS region through Polymerase Chain Reaction - Restriction Fragment Length Polymorphisms (PCR-RFLP), it was found out that a majority of the nodulating rhizobia was classified under the genus Bradyrhizobium and the non-nodulating rhizobia was classified under the genus of Sinorhizobium. The species diversity of nodulating rhizobia on the LUT2 showed the lowest at 0.00 whereas the LUT1 showed the highest diversity at 0.87. Similarly, the lowest species diversity of the non-nodulating rhizobia was found on the LUT2 at 0.00 but the highest was obtained from the LUT3 at 0.69. These results suggest that the nodulating rhizobia in this study may have preference with rice-based cropping pattern than with the two cropping systems. On the other hand, the diversity of rhizobia observed on LUT2 indicated that soybean monocropping may have resulted to a lesser diversity of both nodulating and non-nodulating rhizobia.Thus, it can be stated that the change in land utilization even in an agriculture land-use, species diversification and population dominance of certain rhizobia may occur.

Microbial community structural and functional differentiation in capped thickened oil sands tailings planted with native boreal species.

The oil sands mining operations in Alberta have produced billions of m3 of tailings which must be reclaimed and integrated into various mine closure landforms, including terrestrial landforms. Microorganisms play a central role in nutrient cycling during the reclamation of disturbed landscapes, contributing to successful vegetation restoration and long-term sustainability. However, microbial community succession and response in reconstructed and revegetated tailings remain largely unexplored. This study aimed to monitor the structural and functional responses of microbial communities in tailings subjected to different capping and vegetation strategies over two growing seasons (GS). To achieve this, a column-based greenhouse experiment was conducted to investigate microbial communities in tailings that were capped with a layer (10 or 30 cm) of peat-mineral mix (PMM) and planted with either upland or wetland communities. DNA metabarcoding analysis of the bacterial 16S rRNA gene and fungal ITS2 region as well as shotgun metagenomics were used to asses the impact of treatments on microbial taxonomy and functions, respectively. Results showed that tailings microbial diversity and community composition changed considerably after two GS compared to baseline samples, while communities in the PMM capping layer were much more stable. Likewise, several microbial functions were significantly enriched in tailings after two GS. Interestingly, the impact of capping on bacterial communities in tailings varied depending on the plant community, leading to a higher number of differentially abundant taxa and to a decrease in Shannon diversity and evenness in the upland treatment but not in the wetland treatment. Moreover, while capping in the presence of wetland vegetation increased the energy-related metabolic functions (carbon, nitrogen, and sulfur), these functions were depleted by capping in the upland treatment. Fungi represented a small proportion of the microbial community in tailings, but the relative abundance of several taxa changed over time, while the capping treatments favored the growth of some beneficial taxa, notably the root endophyte Serendipita, in both upland and wetland columns. The results suggest that selecting the right combination of capping material and vegetation type may contribute to improve below-ground microbial processes and sustain plant growth in harsh environments such as oil sands tailings.

Dynamics of Fine Root Decomposition in Different Vegetation Types: Investigating the Impact of Soil Fungal Communities and Enzyme Activities

Fine root decomposition plays a vital role in driving the carbon cycle in terrestrial ecosystems, as it constitutes a substantial part of annual net primary production and, as transient tissues, returns to the soil within relatively short timescales. Soil fungal communities and enzyme activities strongly influence this process. In this study, we used an in situ soil core decomposition method to compare the fine root decomposition rates of Liriodendron chinense (Hemsl.) Sargent, Cunninghamia lanceolata (Lamb.) Hook, and Phyllostachys edulis (Carrière) J.Houz forests over a 1-year period (March 2021–March 2022). We quantified the chemical attributes of fine roots and soil enzymatic activities across different forests, detected fungal communities via ITS rRNA gene sequencing, and forecasted fungal functional groups using the FUNGuild database. The results showed that fine root decomposition was fastest in the Liriodendron chinense (Hemsl.) Sargent forest (77.2%) and the slowest for Cunninghamia lanceolata (Lamb.) Hook (59.2%). Structural equation modeling (SEM) results indicated that the carbon content of fine roots and the functional groups of soil fungi are crucial to fine root decomposition. They not only directly influence fine root decomposition but also promote it through soil enzymatic activities, clearly suggesting that changes in soil enzymatic activities can be employed to explain the ecological effects of the root decomposition process. This study illuminates significant differences in the chemical characteristics of fine roots, soil enzymatic activities, and soil fungal communities among different forest types, all of which significantly affect fine root decomposition.

Conserved organ-specific microbial assemblages in different populations of a terrestrial crab.

Microorganisms are ubiquitous in the environment and provide genetic and physiological functions to multicellular organisms. Knowledge on the associated microbiota is becoming highly relevant to understand the host's ecology and biology. Among invertebrates, many examples of endosymbiosis have been described, such as those in corals, ants, and termites. At present, however, little is known on the presence, diversity, and putative roles of the microbiota associated to brachyuran crabs in relation to their environment. In this work we investigated the associated microbiota of three populations of the terrestrial brachyuran crab Chiromantes haematocheir to find evidence of a conserved organ-specific microbiome unrelated to the population of origin and dissimilar from environmental microbial assemblages. Bacterial 16S rRNA gene and fungal ITS sequences were obtained from selected crab organs and environmental matrices to profile microbial communities. Despite the presence of truly marine larval stages and the absence of a gregarious behaviour, favouring microbiota exchanges, we found common, organ-specific microbiota, associated with the gut and the gills of crabs from the different populations (with more than 15% of the genera detected specifically enriched only in one organ). These findings suggest the presence of possible functional roles of the organ-specific microbiota.

Dodder Parasitism Leads to the Enrichment of Pathogen Alternaria and Flavonoid Metabolites in Soybean Root

Dodders (Cuscuta chinensis) are rootless and holoparasitic herbs that can infect a variety of host plants, including the vitally important economic and bioenergy crop soybean (Glycine max). Although dodder parasitism severely affects the physiology of host plants, little is known about its effects on fungal communities and root secondary metabolites in hosts. In this study, variations in root-associated fungal communities and root metabolites of soybean under different parasitism conditions were investigated using ITS rRNA gene sequencing and UPLC–MS/MS metabolome detection technologies. The results showed that dodder parasitism significantly altered the composition and diversity of the fungal communities in the rhizosphere and endosphere of soybean. The relative abundance of the potential pathogenic fungus Alternaria significantly increased in the root endosphere of dodder-parasitized soybean. Furthermore, correlation analysis indicated that the fungal community in the root endosphere was susceptible to soil factors under dodder parasitism. Meanwhile, the content of soil total nitrogen was significantly and positively correlated with the relative abundance of Alternaria in the rhizosphere and endosphere of soybean. Metabolomic analysis indicated that dodder parasitism altered the accumulation of flavonoids in soybean roots, with significant upregulation of the contents of kaempferol and its downstream derivatives under different parasitism conditions. Taken together, this study highlighted the important role of dodder parasitism in shaping the fungal communities and secondary metabolites associated with soybean roots, providing new insights into the mechanisms of multiple interactions among dodder, soybean, microbial communities and the soil environment.

Diversity of fungal microbiome obtained from plant rhizoplanes

Microbial communities, and their ecological importance, have been investigated in several habitats. However, so far, most studies could not describe the closest microbial interactions and their functionalities. This study investigates the co-occurring interactions between fungi and bacteria in plant rhizoplanes and their potential functions. The partnerships were obtained using fungal-highway columns with four plant-based media. The fungi and associated microbiomes isolated from the columns were identified by sequencing the ITS (fungi) and 16S rRNA genes (bacteria).Statistical analyses including Exploratory Graph and Network Analysis were used to visualize the presence of underlying clusters in the microbial communities and evaluate the metabolic functions associated with the fungal microbiome (PICRUSt2). Our findings characterize the presence of both unique and complex bacterial communities associated with different fungi. The results showed that Bacillus was associated as exo-bacteria in 80 % of the fungi but occurred as putative endo-bacteria in 15 %. A shared core of putative endo-bacterial genera, potentially involved in the nitrogen cycle was found in 80 % of the isolated fungi. The comparison of potential metabolic functions of the putative endo- and exo-communities highlighted the potential essential factors to establish an endosymbiotic relationship, such as the loss of pathways associated with metabolites obtained from the host while maintaining pathways responsible for bacterial survival within the hypha.

Long-term prednisone treatment causes fungal microbiota dysbiosis and alters the ecological interaction between gut mycobiome and bacteriome in rats.

Glucocorticoids (GCs) are widely used in the treatment of immune-mediated diseases due to their anti-inflammatory and immunosuppressive effects. Prednisone is one of the most commonly used GCs. However, it is still unknown whether prednisone affects gut fungi in rats. Herein we investigated whether prednisone changed the composition of gut fungi and the interactions between gut mycobiome and bacteriome/fecal metabolome in rats. Twelve male Sprague-Dawley rats were randomly assigned to a control group and a prednisone group which received prednisone daily by gavage for 6 weeks. ITS2 rRNA gene sequencing of fecal samples was performed to identify differentially abundant gut fungi. The associations between gut mycobiome and bacterial genera/fecal metabolites obtained from our previously published study were explored by using Spearman correlation analysis. Our data showed that there were no changes in the richness of gut mycobiome in rats after prednisone treatment, but the diversity increased significantly. The relative abundance of genera Triangularia and Ciliophora decreased significantly. At the species level, the relative abundance of Aspergillus glabripes increased significantly, while Triangularia mangenotii and Ciliophora sp. decreased. In addition, prednisone altered the gut fungi-bacteria interkingdom interactions in rats after prednisone treatment. Additionally, the genus Triangularia was negatively correlated with m-aminobenzoic acid, but positively correlated with hydrocinnamic acid and valeric acid. Ciliophora was negatively correlated with phenylalanine and homovanillic acid, but positively correlated with 2-Phenylpropionate, hydrocinnamic acid, propionic acid, valeric acid, isobutyric acid, and isovaleric acid. In conclusion, long-term prednisone treatment caused fungal microbiota dysbiosis and might alter the ecological interaction between gut mycobiome and bacteriome in rats.

Differential distribution patterns and assembly processes of soil microbial communities under contrasting vegetation types at distinctive altitudes in the Changbai Mountain.

Diversity patterns and community assembly of soil microorganisms are essential for understanding soil biodiversity and ecosystem processes. Investigating the impacts of environmental factors on microbial community assembly is crucial for comprehending the functions of microbial biodiversity and ecosystem processes. However, these issues remain insufficiently investigated in related studies despite their fundamental significance. The present study aimed to assess the diversity and assembly of soil bacterial and fungal communities to altitude and soil depth variations in mountain ecosystems by using 16S and ITS rRNA gene sequence analyses. In addition, the major roles of environmental factors in determining soil microbial communities and assembly processes were further investigated. The results showed a U-shaped pattern of the soil bacterial diversity at 0-10 cm soil depth along altitudes, reaching a minimum value at 1800 m, while the fungal diversity exhibited a monotonically decreasing trend with increasing altitude. At 10-20 cm soil depth, the soil bacterial diversity showed no apparent changes along altitudinal gradients, while the fungal Chao1 and phylogenetic diversity (PD) indices exhibited hump-shaped patterns with increasing altitude, reaching a maximum value at 1200 m. Soil bacterial and fungal communities were distinctively distributed with altitude at the same depth of soil, and the spatial turnover rates in fungi was greater than in bacteria. Mantel tests suggested soil physiochemical and climate variables significantly correlated with the β diversity of microbial community at two soil depths, suggesting both soil and climate heterogeneity contributed to the variation of bacterial and fungal community. Correspondingly, a novel phylogenetic null model analysis demonstrated that the community assembly of soil bacterial and fungal communities were dominated by deterministic and stochastic processes, respectively. The assembly processes of bacterial community were significantly related to the soil DOC and C:N ratio, while the fungal community assembly processes were significantly related to the soil C:N ratio. Our results provide a new perspective to assess the responses of soil microbial communities to variations with altitude and soil depth.

Two new species of sedentary nematodes of the genus Meloidodera Chitwood, Hannon & Esser, 1956 (Tylenchida: Heteroderidae) from Mexico

Summary Two new species of the genus Meloidodera collected in Mexico are described here: M. ferrisi sp. n. parasitising roots of an oak tree in the State of Mexico and M. tecoacensis sp. n. parasitising roots of buffalo bur nightshade in the Tlaxcala State. Meloidodera ferrisi sp. n. is characterised by a spherical female body covered completely by a dark thick cuticular layer, length/width of the female body = 0.8-1.6, stylet = 35-43 μm and second-stage juvenile with average body = 340 μm and average tail length = 35.6 μm. Meloidodera tecoacensis sp. n. is characterised by the female having a spherical body covered with a yellow transparent material, length/width of the female body = 1.1-2.8, stylet = 20-33 μm and second-stage juvenile with average body = 340 μm and average tail length = 29.8 μm. These two species were molecularly characterised using the D2-D3 expansion segments of 28S rRNA, ITS rRNA and COI gene sequences. Phylogenetic analysis revealed that the two new species represent a separate evolutionary lineage within the subfamily Meloidoderinae. An identification key for 12 Meloidodera species is provided.

Piriformospora indica alter root-associated microbiome structure to enhance Artemisia annua L. tolerance to arsenic

Microorganisms in the rhizosphere are crucial allies for plant stress tolerance. Recent research suggests that by interacting with the rhizosphere microbiome, microorganisms can aid in the revegetation of soils contaminated with heavy metal(loid)s (HMs). However, it is unknown that how Piriformospora indica influences the rhizosphere microbiome to mitigate arsenic-toxicity in arsenic-enriched environments. Artemisia annua plants were grown in the presence or absence of P. indica and spiked with low (50) and high (150 µmol/L) concentrations of arsenic (As). After inoculation with P. indica, fresh weight increased by 37.7% and 10% in control and high concentration treated plants, respectively. Transmission electron microscopy showed that cellular organelles were severely damaged by As and even disappeared under high concentration. Furthermore, As was mostly accumulated by 5.9 and 18.1 mg/kg dry weight in the roots of inoculated plants treated with low and high concentrations of As, respectively. Additionally, 16 S and ITS rRNA gene sequencing were applied to analyze the rhizosphere microbial community structure of A. annua under different treatments. A significant difference was observed in microbial community structure under different treatments as revealed by non-metric multidimensional scaling ordination. The bacterial and fungal richness and diversity in the rhizosphere of inoculated plants were actively balanced and regulated by P. indica co-cultivation. Lysobacter and Steroidobacter were found to be the As-resistant bacterial genera. We conclude that P. indica inoculation could alter rhizosphere microecology, thereby mitigating As-toxicity without harming the environment.

Morphological and molecular identification of three new resupinate species of Hyphoderma (Hyphodermataceae, Agaricomycetes) from East Asia

The genus Hyphoderma is one of the most important corticioid fungi worldwide, which causes white rot in wood and plays an important role in forest ecosystems and carbon cycle. In this study, three new wood-inhabiting fungal species, H. marginatum, H. tropicum and H. yunnanense are proposed based on a combination of the morphological and molecular evidence. Hyphoderma marginatum is characterized by the cracking, hard fragile basidiomata having smooth hymenial surface with the upwarping margin, a monomitic hyphal system with clamped generative hyphae, and cylindrical basidiospores. Hyphoderma tropicum is characterized by the resupinate basidiomata with tuberculate hymenial surface, presence of the moniliform cystidia, and ellipsoid to cylindrical basidiospores (6.5–7.5 × 3–4 µm), Hyphoderma yunnanense is characterized by the corneus basidiomata, presence of clamped septate cystidia, and ellipsoid to cylindrical basidiospores. Sequences of ITS and nLSU rRNA genes were used for phylogenetic analyses using maximum likelihood, maximum parsimony, and Bayesian inference methods. The three new species of Hyphoderma inferred from ITS sequences and form separate lineages within the genus.

Composition, Abundance, and Diversity of the Soil Microbiome Associated with the Halophytic Plants Tamarix aphylla and Halopeplis perfoliata on Jeddah Seacoast, Saudi Arabia

The coast of the Red Sea in Jeddah City is home to a unique microbial community that has adapted to extreme environmental conditions. Therefore, it is essential to characterize the microbial community in this unique microbiome to predict how environmental changes will affect it. The aim of this study was to conduct metagenomic sequencing of 16S rRNA and ITS rRNA genes for the taxonomic classification of the microbial community in soil samples associated with the halophytic plants Tamarix aphylla and Halopeplis perfoliata. Fifteen soil samples were collected in triplicate to enhance robustness and minimize sampling bias. Firstly, to identify novel microbial candidates, the gDNAs were isolated from the saline soil samples surrounding each plant, and then bacterial 16S (V3–V4) and fungal ITS1 regions were sequenced utilizing a high-throughput approach (next-generation sequencing; NGS) on an Illumina MiSeq platform. Quality assessment of the constructed amplicon libraries was conducted using Agilent Bioanalyzer and fluorometric quantification methods. The raw data were processed and analyzed using the Pipeline (Nova Lifetech, Singapore) for bioinformatics analysis. Based on the total number of readings, it was determined that the phylum Actinobacteriota was the most prevalent in the soil samples examined, followed by the phylum Proteobacteria. Based on ITS rRNA gene analysis, the alpha and beta fungal diversity in the studied soil samples revealed that the fungal population is structured into various groups according to the crust (c) and/or rhizosphere (r) plant parts. Fungal communities in the soil samples indicated that Ascomycota and Basidiomycota were the two most abundant phyla based on the total amount of sequence reads. Secondly, heat-map analysis of the diversity indices showed that the bacterial alpha diversity, as measured by Shannon, Simpson, and InvSimpson, was associated with soil crust (Hc and Tc enclosing H. perfoliata and T. aphylla, respectively) and that the soil rhizosphere (Hr and Tr) was strongly correlated with bacterial beta diversity. Finally, fungal-associated Tc and Hc samples clustered together, according to observations made using the Fisher and Chao1 methods, and Hr and Tr samples clustered together according to Shannon, Simpson, and InvSimpson analyses. As a result of the soil investigation, potential agents that have been identified could lead to innovative agricultural, medical, and industrial applications.

Hawaiian coral holobionts reveal algal and prokaryotic host specificity, intraspecific variability in bleaching resistance, and common interspecific microbial consortia modulating thermal stress responses

Historically, Hawai‘i had few massive coral bleaching events, until two consecutive heatwaves in 2014–2015. Consequent mortality and thermal stress were observed in Kāne‘ohe Bay (O‘ahu). The two most dominant local species exhibited a phenotypic dichotomy of either bleaching resistance or susceptibility (Montipora capitata and Porites compressa), while the third predominant species (Pocillopora acuta) was broadly susceptible to bleaching. In order to survey shifts in coral microbiomes during bleaching and recovery, 50 colonies were tagged and periodically monitored. Metabarcoding of three genetic markers (16S rRNA gene ITS1 and ITS2) followed by compositional approaches for community structure analysis, differential abundance and correlations for longitudinal data were used to temporally compare Bacteria/Archaea, Fungi and Symbiodiniaceae dynamics. P. compressa corals recovered faster than P. acuta and Montipora capitata. Prokaryotic and algal communities were majorly shaped by host species, and had no apparent pattern of temporal acclimatization. Symbiodiniaceae signatures were identified at the colony scale, and were often related to bleaching susceptibility. Bacterial compositions were practically constant between bleaching phenotypes, and more diverse in P. acuta and M. capitata. P. compressa's prokaryotic community was dominated by a single bacterium. Compositional approaches (via microbial balances) allowed the identification of fine-scale differences in the abundance of a consortium of microbes, driving changes by bleaching susceptibility and time across all hosts. The three major coral reef founder-species in Kāne‘ohe Bay revealed different phenotypic and microbiome responses after 2014–2015 heatwaves. It is difficult to forecast, a more successful strategy towards future scenarios of global warming. Differentially abundant microbial taxa across time and/or bleaching susceptibility were broadly shared among all hosts, suggesting that locally, the same microbes may modulate stress responses in sympatric coral species. Our study highlights the potential of investigating microbial balances to identify fine-scale microbiome changes, serving as local diagnostic tools of coral reef fitness.

Distribution of microbial abundance in long-term copper contaminated soils from Topolnitsa-Pirdop valley, Southern Bulgaria

This study presents the distribution of bacterial and fungal abundances in long-term copper (Cu) contaminated soils in Topolnitsa-Pirdop valley – a highly industrialized zone with a number of mines and processing plants for copper and other non-ferrous metals. The bacterial (16S rRNA gene copies) and fungal (ITS rRNA gene copies) were estimated using quantitative PCR technique in five topsoils, differently Cu contaminated (ranging from 28.05 to 198.9 mg kg-1). Bacterial abundance varied in a range of 1.68 × 1011 to 3.24 × 101116S rRNA genes, whereas fungi amounted from 1.95 × 108 to 6.71 × 108 ITS rRNA genes. Fungal and bacterial abundances were significantly (fungi) and insignificantly (bacteria) influenced by Cu contamination. The fungal/bacterial ratio related negatively with soil Cu, which shifted microbial communities’ structure towards bacterial dominance. Since the ratio between bacteria and fungi are vital in explaining many soil functions, the calculated changes in this ratio indicated deterioration in soil quality, being of primary importance for plant production.

The contrasting responses of abundant and rare microbial community structures and co-occurrence networks to secondary forest succession in the subalpine region.

Knowledge of variations in abundant and rare soil microbial communities and interactions during secondary forest succession is lacking. Soil samples were gathered from different secondary successional stages (grassland, shrubland, and secondary forest) to study the responses of abundant and rare bacterial and fungal communities, interactions and driving factors to secondary forest succession by Illumina sequencing of the 16S and ITS rRNA genes. The results showed that the α-diversities (Shannon index) of abundant bacteria and fungi revealed no significant changes during secondary forest succession, but increased significantly for rare bacteria. The abundant and rare bacterial and fungal β-diversities changed significantly during secondary forest succession. Network analysis showed no obvious changes in the topological properties (nodes, links, and average degree) of abundant microbial networks during secondary forest succession. In contrast, these properties of the rare microbial networks in the secondary forest were higher than those in the grassland and shrubland, indicating that rare microbial networks are more responsive to secondary forest succession than abundant microorganisms. Additionally, rare microbial networks revealed more microbial interactions and greater network complexity than abundant microbial networks due to their higher numbers of nodes and links. The keystone species differed between the abundant and rare microbial networks and consisted of 1 and 48 keystone taxa in the abundant and rare microbial networks, respectively. Soil TP was the most important influencing factor of abundant and rare bacterial communities. Successional stages and plant richness had the most important influences on abundant and rare fungal communities, respectively. C:P, SM and N:P were mainly related to abundant and rare microbial network topological properties. Our study indicates that abundant and rare microbial communities, interactions and driving factors respond differently to secondary forest succession.

Sustainability of food side streams: a case study of fermented blends made with sour whey and sunflower press cake powder using the back-slopping technique

The exploitation of by-products is a key factor to increase the sustainability of the agri-food chain and fermentation is a simple and eco-friendly process for achieving safe and suitable food materials. In this study, we investigated the possibility to manage a spontaneous fermentation of blends made with different proportions of two food side streams (bovine acid whey and sunflower press cake powder) through the application of a back-slopping technique of the mixed material incubated at 26°C in static conditions. A full-factorial 2-factor 3-level design of experiment was applied to infer the effect of the percent (w/w) of press cake powder in the mixture (20, 25, and 30%) and the rate of back-slopping inoculum (15, 30, and 45%). The pH value, titratable acidity, content of sugars, organic acids, and phenolic acids, enumeration of lactic acid bacteria, yeasts and molds, bacterial contaminants, presumptive Bacillus cereus, and Escherichia coli were measured for each fermentation step at 0, 24, 48, and 72 h. On the same samples, a metataxonomics analysis, targeted on bacterial 16S rRNA gene and fungal ITS region, was performed by using the Illumina MiSeq platform. Acidification of the blends (on average, starting pH = 5.45 ± 011, final pH = 4.61 ± 0.11; starting acidity =13.68 ± 1.02 °SH/50 mL, final acidity = 28.17 ± 2.92°SH/50 mL) and high LAB counts (on average, 9.39 log CFU/g ± 0.25) were observed at the end of each refreshment. In all fermented mixtures, B. cereus, E. coli, and molds counts were lower than the detection limit (<2 log CFU/g), whereas bacterial contaminants, overall spore-formers, were always present (3.74 log CFU/g ± 0.27). After 72 h, the dropping of pH value was maximum, yielding significant differences compared to previous fermentation steps (p < 0.01); particularly, the lowest pH (4.45 ± 0.06) was achieved in the central points of DoE (25% of press cake powder and 30% of back-slopping rate), representing the most suitable condition. Results from both culture-dependent and -independent techniques were consistent; although Lactococcus lactis, continuously deriving from the acid whey, was the main LAB, Pediococcus pentosaceus appeared and, in some cases, became the dominant species. Finally, a long-term trial (about 1 month), using the best condition previously pointed out, was performed with an extension of the incubation time to 84 h for each refreshment. The increase in acidity forced the natural selection toward acid-tolerant microbial strains confirming the former results. Although preliminary, these findings can be useful for developing innovative operations to manage these two relevant side streams implementing the circularity of food resources.

Characterization of Yeast Isolated from Berkeep, a Traditional Fermented Milk Products of Darfur State, Western Sudan

Berkeep is a naturally fermented yoghurt-like milk product consumed as common food in parts of the Darfur State, Western Sudan. Its production and consumption derive much food security and economic benefits to the rural people in the region. The objective of this study was to isolate and characterize yeasts of Berkeep by both conventional and molecular-based methods. A total of 220 yeast isolates, were obtained from 75 samples of Berkeep from three production sites namely, Elkoumah, Manwashy and Kass in Darfur state, were purified then characterized to species level by molecular tools. Based on ITS-PCR using the forward primer Cy5-Y-ITS1 and reverse primer Y-ITS4, the isolates were screened into five groups. Representative of each group was selected for sequence analysis of ITS rRNA gene. The gene sequence was subjected to nucleotide BLAST. The yeast microbiota of Berkeep was dominated by Kluyveromyces marxianus (YG4, 85 isolates) which showed 100% homology towards Kluyveromyces marxianus isolate QKM4. 14.54% (32 isolates), Sixty-eight (Group YG5) identified as Saccharomyces cerevisiae showed 97.22% homology towards Saccharomyces cerevisiae isolate JKSP39. Group YG3 revealed 100% homology towards Pichia kudriavzevii isolate Sugarcane. Eleven isolates, (YG2) showed 99.37% homology towards Pichia kudriavzevii strain YS179. The twenty-four isolates of group, (YG1) recorded 99.70% similarity towards Candida intermedia isolate B-NC-12-f 16i. Very minute variation was observed with in the three production sites concerning the yeast count and type of yeast species.

The Impact of Storage Temperature on the Development of Microbial Communities on the Surface of Blueberry Fruit.

Microbial contamination is one of the main reasons for the quality deterioration of postharvest blueberries during storage. In this study, we investigated the surface microbiota of blueberry fruits stored at different temperatures via high-throughput sequencing of the 16S and ITS rRNA genes. The results indicated that the α-diversity of the microbial communities in samples stored at 4 °C was much higher than that in samples stored at 25 °C. The composition of the bacterial and fungal communities on the surface of the blueberry fruits varied at different storage temperatures. Ascomycota, Basidiomycota, Anthophyta, Chlorophyta, Proteobacteria, and Cyanobacteria were the most abundant phyla in the bacterial community. Furthermore, five preservation quality indices were measured, and the influence on the α-diversity of the bacterial community was found to be significantly weaker than that of the fungal community. Based on the prediction of the bacterial flora function, the change in blueberry quality during storage was closely related to its surface microbial effect. This study provides a theoretical basis for an understanding of the microbiota on the surface of blueberry fruits to cause fruit spoilage, and the development of a targeted inhibition technology to preserve blueberry fruits under different storage and transportation environments.