Unclassified Fungi Research Articles

Metataxonomic Identification of Microorganisms during the Coffee Fermentation Process in Colombian Farms (Cesar Department).

The metataxonomic diversity and microbial composition of microorganisms during the coffee fermentation process as well as their relationship with coffee quality were determined across 20 farms in the department of Cesar, Colombia, by sampling coffee fruits from Coffea arabica; Var. Castillo General®, Var. Colombia, and Var. Cenicafé 1. In each farm, the fruits were processed and the fermentation process took place between 10 and 42 h following this. Three samples of mucilage and washed coffee seeds were collected per farm during the fermentation process. The microorganisms present in the mucilage were identified using metataxonomic methods by amplifying the 16S rRNA gene for bacteria and ITS for fungi. The microorganisms' morphotypes were isolated and identified. The analysis of bacteria allowed for the identification of the following genera: Gluconobacter, Leuconostoc, Acetobacter, Frateuria, Pantoea, Pseudomonas, Tatumella, and Weisella, as well as unclassified enterobacteria; the Lactobacillacea and Secundilactobacillus families were only identified in the Var. Cenicafé 1. For fungi, the top 11 genera and families found included Hanseniaspora, Candida, Meyerozyma, Wickerhamomyces, Pichia, f-Saccharomycodaceae, f-Nectriciae, unclassified fungi, and Saccharomycetaceae, which were only found in Cenicafé 1. A total of 92% of the coffee samples obtained scored between 80.1 and 84.9, indicating "Very Good" coffee (Specialty Coffee Association (SCA) scale). Farms with the longest fermentation times showed better coffee attributes related to acidity, fragrance, and aroma. During coffee fermentation, there is a central microbiome. The differences between the microorganisms' genera could be influenced by the coffee variety, while the specific conditions of each farm (i.e., altitude and temperature) and its fermentation processes could determine the proportions of and interactions between the microbial groups that favor the sensory characteristics responsible for coffee cup quality.

Microbial diversity and prediction function profiling of microbial communities in rose jam

AbstractThe microbial diversity of rose jam was analyzed by high‐throughput sequencing, along with functional prediction of the bacterial community. The results indicate that Pseudomonas, Pantoea, and Burkholderia emerged were the top three dominant bacterial groups. Proteobacteria was particularly abundant in R4 (99.1%) and R6 (96.12%). Zygosaccharomyces, unclassified fungi, and Botrytis constituted the top three fungal groups. The presence of unclassified OTUs was observed in all samples, particularly in R6 (52.36%), R8 (45.28), and R9 samples (39.57%). Gene prediction using PICRUSt revealed the existence of multiple KEGG functional modules associated with human metabolism in each rose jam sample. The presence of a high abundance of functional genes indicated the microbial community's diverse wide range of microgenetic resources that can be further explored for research purposes. The microbial community found in rose jam exhibits remarkable diversity and encompasses valuable functional information relevant to human health.

A Snapshot of the Microbiome of a Portuguese Abandoned Gold Mining Area

Microbial communities are known to contribute deeply to geochemical cycles, including weathering, protection from erosion and mineral precipitation. Studies aiming to understand mining areas’ microbiomes are of high relevance since they can help pinpoint the occurrence of environmental shifts, key bioremediation species, environmental metals recovery strategies, and microorganisms with relevant industrial properties. Nonetheless, so far, the study of Portuguese gold-rich areas’ microbiomes has been largely neglected. The main goal of this study was to apply high-throughput sequencing methods to study the microbiome (Bacteria and Fungi) and predict their functional/metabolic profiles in an abandoned Portuguese gold mining area (considering zones without a history of mining, the tailings and the flooded mine interior). The results obtained revealed high bacterial and fungal diversities at these sites while also pinpointing the presence of relative homogenous bacterial and heterogenous fungal communities. Areas without mining history were mainly dominated by WD2101 soil groups, Sphingomonas, Candidatus Solibacter, Helotiales, unclassified Fungi and Arxotrichum. The tailings were mainly colonized by Bryobacter, WD2101 soil groups, WPS-2 genera, Starmerella, Helotiales and Mollisia. On the other hand, the mine area displayed a dominance of Crossiella, Gemmataceae, Acidobacteriaceae (Subgroup 1), Acidiphilium, Mortierella, unclassified Fungi and Chaetothyriales. Furthermore, we verified that contrary to bacteria, the fungal structural diversity is somewhat more restricted to each site. In addition, metabolic, functional and ecological profiles revealed a strong distinction for both bacterial and fungal communities while also revealing the presence of well-adapted communities to each of the particular microenvironments considered.

Enhancing Resistance to Salinity in Wheat by Using Streptomyces sp. HU2014

Salt stress affects the growth and global production of wheat (Triticum aestivum L.). Plant growth-promoting microbes can enhance plant resistance to abiotic stresses. In this study, we aimed to assess the inoculation of soil with Streptomyces sp. HU2014 to improve wheat tolerance to salt stress from multiple perspectives, including the interaction of the strain, the addition of NaCl, the condition of the wheat, and rhizosphere microbial communities. The results showed that the strain promoted wheat growth under NaCl stress by increasing biomass by 19.8%, total chlorophyll content by 72.1%, proline content by 152.0%, and malondialdehyde content by 106.9%, and by decreasing catalase by 39.0%, peroxidase by 1.4%, and soluble sugar by 61.6% when compared to the control. With HU2014 soil inoculation, total nitrogen, nitrate nitrogen, total phosphorus, and Olsen phosphorus increased, whereas ammonium nitrogen and pH decreased. HU2014 inoculation and/or the addition of NaCl affected the diversity of rhizosphere bacteria, but not fungi. The structure of the microbial community differed after HU2014 inoculation, with Proteobacteria, Acidobacteriota, Bacteroidota, and unclassified fungi being the dominant phyla, and these taxa correlated with the above-mentioned soil parameters. Thus, this study provided a promising way to enhance wheat tolerance to salt stress and improve the agricultural ecological environment by using plant growth-promoting microbes.

Unraveling the relationship between plant species and physicochemical properties on rhizosphere and rhizoplane fungal communities in alpine wet meadows

BackgroundWet meadows, a type of wetland, are impacted by significant climate fluctuation and human activity, impacting soil microorganisms that play an essential role in ecosystem processes. Understanding the underlying ecological mechanisms and processes of wet meadows depends on the fungal communities associated with the plant roots. We used Illumina MiSeq profiling for amplicon sequencing to determine how environmental factors and elevation affect the fungal communities of the rhizosphere and rhizoplane related to three plant species, Cremanthodium ellisii, Cremanthodium lineare, and Caltha scaposa, in alpine wet meadows.ResultsThe phyla Ascomycota and Basidiomycota dominated the rhizosphere (54.5% and 20.9%) and rhizoplane (51.6% and 36.4%), while the predominant fungal genera in the rhizosphere and rhizoplane were Unclassified fungi, Unclassified Ascomycota, Pseudeurotium, Tetracladium, Vishniacozyma, Rhodotorula, Cadophora, and Penicillium. Mantel test and network analysis revealed that the soil water content (SWC), soil organic carbon (SOC), and total nitrogen (TN) were the primary drivers of fungal communities. However, the influence of microbial biomass C (MBC), pH, microbial biomass N (MBN), and elevation varied. Stochastic assembly processes were dominant in both rhizosphere and rhizoplane fungal communities. FUNGuild functional prediction revealed site-specific variation in the trophic level and guild of plant-root-associated fungal communities. The rhizosphere contained 58.5% saprotrophs, 11.7% pathotrophs, and 12.6% symbiotrophs. In addition, 60.4% of the observed OTUs were arbuscular mycorrhizae, 13.2% were endophytes, 20.9% were ectomycorrhizae, and 1.09% were orchid mycorrhizae. The rhizoplane comprised 51.3% of OTUs linked with saprotrophs, 13.9% with pathotrophs, and 7.92% with symbiotrophs. Moreover, 36.1% of OTUs represented arbuscular mycorrhizae, 25.0% were endophytes, 30.6% were ectomycorrhizae, and 2.77% were ascribed to orchid mycorrhizae in the rhizoplane. The abundance of saprotrophs and pathotrophs in the rhizosphere was highest in C. ellisii at SI and SIII, while symbiotrophs were highest in C. lineare at SIII. Similar variations among the plant species and sites were observed in the fungal functional groups (guilds).ConclusionsIt was concluded that although root compartments significantly influenced the fungal communities in the rhizosphere and rhizoplane, environmental factors and plant types exhibited distinct effects. This study explains how physicochemical properties, plant species, and sites can alter the overall structure and functional repertoire of fungal communities in alpine wet meadows.Graphical

Soil microbial communities as potential regulators of N2O sources in highly acidic soils

• Soil pH was a key driver of N2O emission and sources in acidic soils. • N2O emission was significantly positively associated with the ratio of ITS to 16S. • N2O was significantly correlated with bacterial and fungal community composition. • Fungi contributed to N2O in highly acidic tea plantations and vegetable fields. Acidic soil is a main source of global nitrous oxide (N2O) emissions. However, the mechanism behind the high N2O emissions from acidic soils remains a knowledge gap. The objective of this microcosm incubation study was to pin-point the microbial mechanisms involved in N2O production processes in acidic soils. For that purpose, the isotopic signatures and microbial community structure and composition of four soil samples were examined. The results showed that highly acid soils (pH = 3.51) emitted 89 times more N2O than alkaline soils (pH = 7.95) under the same nitrogen (N) inputs. Fungal denitrification caused high N2O emissions in acidic soils. ITS to 16S abundance ratio was positively correlated with cumulative N2O emissions from the tested soils. The highly acid soils (pH < 4.5) showed greater fungal nirK gene abundance and lower abundance of AOA-amoA, AOB-amoA, nirK, nosZ I and nosZ II genes. The unclassified Aspergillaceae fungi (63.65%) dominated the highly acidic soils and was the most strongly correlated genus with N2O emissions. These findings highlight that soil microbial community structures, denitrifying fungi in particular, shaped by low pH (pH < 4.5) lead to high N2O emissions from acidic soils.

Stochastic processes drive the soil fungal communities in a developing mid-channel bar.

Intricate associations between rhizosphere microbial communities and plants play a critical role in developing and maintaining of soil ecological functioning. Therefore, understanding the assembly patterns of rhizosphere microbes in different plants and their responses to environmental changes is of great ecological implications for dynamic habitats. In this study, a developing mid-channel bar was employed in the Yangtze River to explore the assembly processes of rhizosphere fungal communities among various plant species using high-throughput sequencing-based null model analysis. The results showed a rare significant variation in the composition and alpha diversity of the rhizosphere fungal community among various plant species. Additionally, the soil properties were found to be the primary drivers instead of plant species types. The null model analysis revealed that the rhizosphere fungal communities were primarily driven by stochastic processes (i.e., undominated processes of ecological drift), and the predominance varied with various plant species. Moreover, the assembly processes of rhizosphere fungal communities were significantly related to the changes in soil properties (i.e., soil total carbon, total nitrogen, organic matter, and pH). The co-occurrence network analysis revealed that many keystone species belonged to unclassified fungi. Notably, five network hubs were almost unaffected by the measured soil properties and aboveground plant traits, indicating the effect of stochastic processes on the rhizosphere fungal community assembly. Overall, these results will provide insights into the underlying mechanisms of fungal community assembly in the rhizosphere soils, which are significant for maintaining the functional stability of a developing ecosystem.

High-throughput sequencing reveals omnivorous and preferential diets of the rotifer Polyarthra in situ.

Knowledge of in situ diet of widespread rotifers is crucial for accurately understanding the trophic position, ecological function, and adaptability to environmental changes in aquatic ecosystems. However, it is challenging to achieve the in situ diet information due to the lack of efficient and comprehensive methods. Here, we investigated the diet composition of Polyarthra in a subtropical lake using high-throughput sequencing (HTS) of a rRNA metabarcode for Polyarthra and ambient water samples. After eliminating Polyarthra sequences, a total of 159 operational taxonomic units (OTUs) from taxa in 15 phyla were detected from Polyarthra gut content samples. Most of the OTUs belong to Chlorophyta, followed by unclassified Fungi, Chrysophyta, Dinoflagellata, Ciliophora, Bacillariophyta, Cryptophyta, Arthropoda, Cercozoa, Mollusca, Apicomplexa, Haptophyta, Amoebozoa, Chordata and other eukaryotes. Our results showed that Polyarthra mainly grazed on Chlorophyta, which may result from the high relative abundance of Chlorophyta in ambient waters. In contrast, Chrysophyceae and Synurophyceae were enriched in Polyarthra's gut, indicating that this rotifer prefers these taxa as food. Moreover, correlation analysis showed that total nitrogen, transparency, depth, Chlorophyll-a and total phosphorus were key factors for the variation of the eukaryotic community in the Polyarthra gut contents. When the concentration of nutrients in the water environment decreased, Polyarthra shifted from herbivorous feeding to more carnivorous feeding. Thus, Polyarthra is generally omnivorous but preference for Chrysophytes and Synurophytes, and it responds to the environmental changes by adopting a flexible feeding strategy. This could partly explain why the widespread rotifers have apparently wide tolerance toward spatial and environmental changes.

Temporal dynamics of the chicken mycobiome.

The microbiome is an integral part of chicken health and can affect immunity, nutrient utilization, and performance. The role of bacterial microbiota members in host health is relatively well established, but less attention has been paid to fungal members of the gastrointestinal tract (GIT) community. However, human studies indicate that fungi play a critical role in health. Here, we described fungal communities, or mycobiomes, in both the lumen and mucosa of the chicken ileum and cecum from hatch through 14 days of age. We also assessed the effects of delayed access to feed immediately post-hatch (PH) on mycobiome composition, as PH feed delay is commonly associated with poor health performance. Chicken mycobiomes in each of the populations were distinct and changed over time. All mycobiomes were dominated by Gibberella, but Aspergillus, Cladosporium, Sarocladium, Meyerozyma, and Penicillium were also abundant. Relative abundances of some taxa differed significantly over time. In the cecal and ileal lumens, Penicillium was present in extremely low quantities or absent during days one and two and then increased over time. Meyerozyma and Wickerhamomyces also increased over time in luminal sites. In contrast, several highly abundant unclassified fungi decreased after days one and two, highlighting the need for improved understanding of fungal gut biology. Mycobiomes from chicks fed during the first 2days PH versus those not fed during the first 2days did not significantly differ, except during days one and two. Similarities observed among mycobiomes of fed and unfed chicks at later timepoints suggest that delays in PH feeding do not have long lasting effects on mycobiome composition. Together, these results provide a foundation for future mycobiome studies, and suggest that negative health and production impacts of delayed feeding are not likely related to the development of fungal populations in the GIT.

Impact of Aspect on Arbuscular Mycorrhizal Fungal Diversity and Community Composition in a Natural Toona ciliata var. pubescens Forest in Subtropical China

The aspect can affect plant communities and soil physical and chemical properties through different microclimates. However, little is known about the effect of aspect on arbuscular mycorrhizal (AM) fungal diversity and community composition, although AM fungi are beneficial for plant nutrient absorption and natural restoration. In this study, AM fungal community and diversity distribution patterns in the rhizosphere soil and roots of seven widespread plants in a natural Toona ciliata var. pubescens (Tc) forest on the north-facing (NF) aspect and south-facing (SF) aspect were investigated using Illumina PE250 high-throughput sequencing in the Guanshan National Nature Reserve, Jiangxi Province, China. Our results exhibited that aspect did not affect AM fungal diversity but significantly affected AM fungal community structure and composition. Glomeraceae was the most common and abundant family in the Tc natural forest. The Glomeromycota sequence proportion of root AM fungal community was significantly larger on NF than on SF (p &lt; 0.05). The relative abundance of Acaulosporaceae of root AM fungal community differed significantly with aspect, being greater on NF than on SF (p &lt; 0.05). In addition, the number of Glomeromycota sequences was significantly larger on SF than on NF, while the number of OTUs and the relative abundance of unclassified fungi in rhizosphere soil in Tc showed the opposite trend (p &lt; 0.05). The soil properties (organic matter, nitrogen, potassium, phosphorus, and pH) were significantly correlated with these changes. These findings indicate that the habitat of NF with low insolation, high soil moisture, and high nutrient content might promote the functional realization of AM fungi; the habitat of SF with high insolation, low soil moisture, and low soil nutrient content might be beneficial for the proliferation and preservation of AM fungal groups. This study provides important information on the ecological processes of AM fungal community construction and microbiological mechanisms in natural Tc forests.

Green Manure Return Strategies to Improve Soil Properties and Spring Maize Productivity under Nitrogen Reduction in the North China Plain

In order to study the effect of green manure return for stabilized spring maize (Zea mays L.) grain yield (GY) we reduced nitrogen fertilizer input by regulation and examined effects on soil nutrients, enzyme activity, and fungal communities. This two-year field experiment was conducted in the North China Plain. The field experiment was undertaken with a split-plot design; the primary plots were winter fallow (WF) and green manure (GM), and the split-plots were five N application rates of 0 (N0), 189 (N189), 216 (N216), 243 (N243), and 270 (N270) kg ha−1. The results showed that, spring maize GY under GM treatments (GYGM) were significantly increased by 5.38–11.68% more than WF treatment (GYWF), and GYWF and GYGM significantly increased by 35.9–91.5% and 80.1–135.5% across all N treatments. By linear-platform model analysis, spring maize under GM treatments obtained higher GY, reaching 1270.5–14,312.2 kg ha−1 with optimized N application rate at 238–265 kg ha−1, which resulted in a GY higher than WF (11,820.0 and 13,654.2 kg ha−1) and N reduced 11.2% (238 vs. 268 kg ha−1). GM treatment significantly increased soil organic carbon by 3.90–12.23% more than WF over all N application rates, and total nitrogen and available nitrogen were significantly increased by 3.79–15.76% and 4.87–17.29%, with total phosphorus and available phosphorus for GM higher than WF by 6.1–13.6% and 9.6–5.3%, respectively. However, there were lesser effects of GM on total potassium and available potassium. Compared to WF, soil catalase, sucrose, urease, and alkaline phosphatase activity were significantly increased by 6.2–16.4%, 5.8–48.1%, 3.3–21.5% and 11.5–82.3%, respectively, over all N application rates under GM over two years. GM increased Zygomycota and Basidiomycota relative abundances significantly, and reduced Thielavia, unclassified fungi, and Podospora relative abundances by 35.35%, 52.92% and 52.77% more than WF treatment, respectively. In summary, due to the GM return into fields, increased soil nutrients were available, which were positively affected by soil enzyme activity and fungal communities, and reduced nutrient requirements, and so the farmers could obtain a spring maize grain yield higher than 14,000 kg ha−1 with a reduced 11.2% N application rate from 268 kg ha−1 to 238 kg ha−1 by sowing winter green manure for a long time period in the North China Plain.

Network analysis reveals the root endophytic fungi associated with Fusarium root rot invasion

Root rot caused by Fusarium sp., a ubiquitous soilborne disease, leads to huge economic losses for tobacco cultivation in China. However, comprehensive knowledge about the interactions between this fungal pathogen and other members of soil and endophytic fungal communities is very limited. In this study, how the invasion process of root rot disease affect the fungal communities of soils and endophytes was systematically studied by using both internal transcribed spacer (ITS) sequencing and molecular ecological network analysis (MENA). The root endophytic fungal community diversity of root rot was 23.99 % and 76.27 % higher than healthy roots according to Shannon and Inv-Simpson indices, respectively. By integrating both community composition analysis and field disease symptoms, the root rot pathogen of this study was identified as Fusarium oxysporum f. sp. psidii. Soil and endophytic fungal communities affected by this pathogen showed more complex network structures and greater number of interaction relationships than those of healthy plants. Besides, the pathogen F. oxysporum had successfully invaded the roots and become a keystone species of endophytic fungal community during the invasion process. In addition, the genera Haematonectria and Ceratobasidium were positively correlated with the pathogen while the genera Eupenicillium, Alternaria, and two unclassified fungi were negatively correlated with the pathogen in the networks of infected roots. These fungi may play important roles in assisting and resisting root rot pathogen invasion, respectively.

Composition and Diversity of the Culturable Endophytic Community of Six Stress-Tolerant Dessert Plants Grown in Stressful Soil in a Hot Dry Desert Region.

Saudi Arabia is part of a hot dry desert region and is characterized by stressful conditions. The main goal of this research was to identify endophytic fungal (EF) community composition, diversity and abundance in relation to their plant hosts and soil stress. The above-ground parts of six wild plants (Haloxylon salicornicum, Salsola kali, Heliotropium bacciferum, Erica verticillata, Salsola imbricata and Bienertia sinuspersici) were sampled, surface-sterilized and cut into small pieces, which were cultured and incubated for 4–6 weeks. Isolates were grouped and identified by using both morphological and ITS rDNA molecular data. The diversity and community structure of plant-endophyte associations were studied. A total of 455 EF isolates were grouped into 25 different taxa; 21 of which were identified at the species level, 2 at genus level and 2 were unclassified fungi. Here, 95.65% of the identified genera were Ascomycota; of which 36.36, 31.81 and 31.81% were members of the classes Dothideomycetes, Eurotiomycetes and Sordariomycetes, respectively. S. imbricata showed the highest isolation rate and colonization frequency (CF%) of EF when compared to other plant species. Additionally, S. imbricata demonstrated the highest species richness and species diversity of the EF community predominated by the genus Fusarium. Conclusively, the core culturable EF genera of six wild plants were identified (unculturable taxa were not identified in this study). The composition of the EF community was revealed to have a strong correlation to both the electrical conductivity and pH of the soil and a moderate correlation to both the host species and the host family. The abundance and diversity of EF communities of the six plants were environment-dependent.

Ammonia-oxidizing bacteria and fungal denitrifier diversity are associated with N2O production in tropical soils

Nitrous oxide (N2O) production in tropical soils cultivated with sugarcane is associated with ammonia-oxidizing bacteria (AOB) and fungal denitrifiers. However, the taxonomic identities and the community diversities, compositions, and structures of AOB and fungal denitrifiers in these soils are not known. Here, we examined the effects of applying different concentrations of an organic recycled residue (vinasse: regular non-concentrated or 5.8-fold concentrated) on the dynamics of AOB and fungal denitrifier community diversity and composition and greenhouse gas emissions during the sugarcane cycle in two different seasons, rainy and dry. DNA was extracted from soil samples collected at six timepoints to determine the dynamics of amoA-AOB and nirK-fungal community diversity and composition by amplicon sequencing with gene-specific primers. Bacterial and archaeal amoA, fungal and bacterial nirK, bacterial nirS and nosZ, total bacteria (16S rRNA) and total fungi (18S rRNA) were quantified by real-time PCR, and N2O and CO2 emissions were measured. The genes amoA-AOB and bacterial nirK clade II correlated with N2O emissions, followed by fungal nirK. The application of inorganic nitrogen fertilizer combined with organic residue, regardless of concentration, did not affect the diversity and structure of the AOB and fungal denitrifier communities but increased their abundances and N2O emissions. Nitrosospira sp. was the dominant AOB, while unclassified fungi were the dominant fungal denitrifiers. Furthermore, the community structures of AOB and fungal denitrifiers were affected by season, with dominance of uncultured Nitrosospira and unclassified fungi in the rainy season and the genera Nitrosospira and Chaetomium in the dry season. Nitrosospira, Chaetomium, Talaromyces purpureogenus, and Fusarium seemed to be the main genera governing N2O production in the studied tropical soils. These results highlight the importance of deciphering the main players in N2O production and demonstrate the impact of fertilization on soil microbial N functions.

Different responses of bacteria and fungi to environmental variables and corresponding community assembly in Sb-contaminated soil

Bacterial communities in antimony (Sb) polluted soils have been well addressed, whereas the important players fungal communities are far less studied to date. Here, we report different responses of bacterial and fungal communities to Sb contamination and the ecological processes controlling their community assembly. Soil samples in the Xikuangshan mining area were collected and subjected to high through-put sequencing of 16S rRNA and ITS1 to investigate bacterial and fungal communities, respectively, along an Sb gradient. Sb speciation in the soil samples and other physicochemical parameters were analyzed as well. Bacterial communities were dominated by Deltaproteobacteria in the soil with highest Sb concentration, whereas Chloroflexi were dominant in the soil with lowest Sb concentration. Fungal communities in high-Sb soils were predominated by unclassified Fungi, whilst Leotiomycetes were dominant in low-Sb soil samples. Multivariate analysis indicated that Sb, pH and soil texture were the main drivers to strongly impact microbial communities. We further identified Sb-resistant microbial groups via correlation analysis. In total, 18 bacterial amplicon sequence variants (ASVs) were found to potentially involve in biogeochemical cycles such as Sb oxidation, sulfur oxidation or nitrate reduction, whereas 12 fungal ASVs were singled out for potential heavy metal resistance and plant growth promotion. Community assembly analysis revealed that variable selection contributed 100% to bacterial community assembly under acidic or high Sb concentration conditions, whereas homogeneous selection dominated fungal community assembly with a contribution over 78.9%. The community assembly of Sb-resistant microorganisms was mainly controlled by stochastic process. The results offer new insights into microbial ecology in Sb-contaminated soils, especially on the different responses of microbial communities under identical environmental stress and the different ecological processes underlining bacterial and fungal community assembly.

Characteristics of soil microbial communities in different restoration models in the ecological immigrants' emigration area in southern Ningxia, China

To reveal the effects of plantations on soil microbial environment,the composition and diversity of soil fungi and bacterial communities in five restoration models (Robinia pseudoacacia, Populus hopeiensis, Pinus tabuliformis, Picea crassifolia, natural restoration) in the mountainous area of southern Ningxia were compared by using high-throughput sequencing technology. The correlation between soil physical-chemical properties and dominant microbial groups was analyzed. The results showed that: 1) Dominant fungi in different restoration models were Ascomycota, Basidiomycota, Mortierellomycota, and unclassified fungi, which accounted for 90% of total fungal community. The dominant soil bacteria were Actinobacteria, Proteobacteria, Acidobacteriota, Chloroflexi, and other bacteria, accounting for more than 80% of total bacterial community. 2) The diversity of soil fungi in P. tabuliformis forest was the highest, with Shannon index, and Simpson index being 3.72±0.37 and 0.07±0.04, respectively. The richness of fungi in naturally restored forest land was the highest, with Ace and Chao1 index of 708.19±137.25 and 706.26±125.34, respectively. The bacterial diversity and richness of species in P. tabuliformis forest land was the highest. The Shannon, Simpson, Ace and Chao1 indices were 6.57±0.04, 0.004±0.00, 3439.81±41.67, 3463.14±32.16, respectively. 3) The fungus with significant difference among restoration models were Solicoccozyma, Cladosporium, and Alternaria. Bacteria from Norank_f_67-14, Rubrobacter_f_Rubrobacteraceae, Sphingomonas_f_Sphingomonadaceae had significant difference among restoration models. 4) The RDA ordination of the dominant microbial flora and soil physical-chemical properties showed that soil bulk density (BD), carbon to nitrogen ratio (C/N), and pH were the major factors affecting the dominant fungal flora. BD, nitrogen to phosphorus ratio (N/P), total phosphorus (TP), and total carbon (TC) were the main factors affecting the dominant bacterial flora. In general, the difference of composition and diversity in the fungal community of different restoration models was higher than that of the bacterial community, indicating that the fungal communities were more sensitive to the changes of tree species and soil environment than bacterial communities. Our results could provide the theoretical foundation for vegetation restoration measures and the maintenance of ecosystem function stability in southern Ningxia.

Salinity is the major driver of the global eukaryotic community structure in fish-canning wastewater treatment plants

Fish-canning wastewater is characterized frequently by a high content of salt (NaCl), making its treatment particularly difficult; however, the knowledge of the effect of NaCl on eukaryotic communities is very limited. In the present study, the global diversity of eukaryotes in activated sludges (AS) from 4 different wastewater treatment plants (WWTPs) treating fish-canning effluents varying in salinity (0.47, 1.36, 1.72 and 12.76 g NaCl/L) was determined by sequencing partial 18S rRNA genes using Illumina MiSeq. A greater diversity than previously reported was observed in the AS community, which comprised 37 and 330 phylum-like and genera-like groups, respectively. In this sense, the more abundant genus-like groups (average relative abundance (RA) > 5%) were Adineta (6.80%), Lecane (16.80%), Dictyostelium (7.36%), Unclassified_Fungi7 (6.94%), Procryptobia (5.13) and Oocystis (5.07%). The eukaryotic communities shared a common core of 25 phylum-like clades (95% of total sequences); therefore, a narrow selection of the eukaryotic populations was found, despite the differences in the abiotic characteristics of fish-canning effluents and reactor operational conditions inflicted. The differences in NaCl concentration were the main factor that influenced the structure of the eukaryotic community, modulating the RAs of the different phylum-like clades of the common core. Higher levels of salt increased the RAs of Ascomycota, Chlorophyta, Choanoflagellata, Cryptophyta, Mollusca, Nematoda, Other Protists and Unclassified Fungi. Among the different eukaryotic genera here found, the RA of Oocystis (Chlorophyta) was intimately correlated to increasing NaCl concentrations and it is proposed as a bioindicator of the global eukaryotic community of fish-canning WWTPs.

Microbial Community Composition Correlates with Metal Sorption in an Ombrotrophic Boreal Bog: Implications for Radionuclide Retention

Microbial communities throughout the 6.5 m depth profile of a boreal ombrotrophic bog were characterized using amplicon sequencing of archaeal, fungal, and bacterial marker genes. Microbial populations and their relationship to oxic and anoxic batch sorption of radionuclides (using radioactive tracers of I, Se, Cs, Ni, and Ag) and the prevailing metal concentrations in the natural bog was investigated. The majority of the detected archaea belonged to the Crenarchaeota, Halobacterota, and Thermoplasmatota, whereas the fungal communities consisted of Ascomycota, Basidiomycota, and unclassified fungi. The bacterial communities consisted mostly of Acidobacteriota, Proteobacteria, and Chloroflexi. The occurrence of several microbial genera were found to statistically significantly correlate with metal concentrations as well as with Se, Cs, I, and Ag batch sorption data. We suggest that the metal concentrations of peat, gyttja, and clay layers affect the composition of the microbial populations in these nutrient-low conditions and that particularly parts of the bacterial and archaeal communities tolerate high concentrations of potentially toxic metals and may concurrently contribute to the total retention of metals and radionuclides in this ombrotrophic environment. In addition, the varying metal concentrations together with chemical, mineralogical, and physical factors may contribute to the shape of the total archaeal and bacterial populations and most probably shifts the populations for more metal resistant genera.

Petroleum contamination significantly changes soil microbial communities in three oilfield locations in Delta State, Nigeria.

Soil microbial community structure is altered by petroleum contamination in response to compound toxicity and degradation. Understanding the relation between petroleum contamination and soil microbial community structure is crucial to determine the amenability of contaminated soils to bacterial- and fungal-aided remediation. To understand how petroleum contamination and soil physicochemical properties jointly shaped the microbial structure of soils from different oilfields, high-throughput sequencing of 16S and ITS amplicons were used to evaluate the shifts of microbial communities in the petroleum-contaminated soils in Ughelli East (UE), Utorogu (UT), and Ughelli West (UW) oilfields located in Delta State, Nigeria. The results showed 1515 bacteria and 919 fungal average OTU number, and community richness and diversity, trending as AL > UT > UW > UE and AL > UW > UT > UE for bacteria, and AL > UW > UT > UE and UW > UT > AL > UE for fungi, respectively. The bacterial taxa KCM-B-112, unclassified Saccharibacteria, unclassified Rhizobiales, Desulfurellaceae, and Acidobacteriaceae and fungal Trichocomaceae, unclassified Ascomycota, unclassified Sporidiobolales, and unclassified Fungi were found to be the dominant families in petroleum-contaminated soils. Redundancy analysis (RDA) and Spearman's correlation analysis revealed that total carbon (TC), electric conductivity (EC), pH, and moisture content (MO) were the major drivers of bacterial and fungal communities, respectively. Gas chromatography-mass spectrophotometer (GC-MS) analysis exhibited that the differences in C7-C10, C11-C16, and C12-C29 compounds in the crude oil composition and soil MO content jointly constituted the microbial community variance among the contaminated soils. This study revealed the bacterial and fungal communities responsible for the biodegradation of petroleum contamination from these oilfields, which could serve as biomarkers to monitor oil spill site restoration within these areas. Further studies on these contaminated sites could offer useful insights into other contributing factors such as heavy metals.

Patterns of Sediment Fungal Community Dependent on Farming Practices in Aquaculture Ponds.

Despite fungi playing an important role in nutrient decomposition in aquatic ecosystems and being considered as vital actors in the ecological processes, they received limited attention regarding the community in aquaculture pond sediments which are extremely important and typically disturbed habitats. Using an ITS1 region of fungal rDNA, this study aimed to investigate sediment fungal communities in fish, crab, and crayfish ponds for decades of farming practices at representative aquaculture regions in the middle Yangtze River basin, China. We then aimed to explore the community patterns associated with species-based farming practices in the ponds at 18 farms. The results showed that the pond sediments harbored more than 9,000 operational taxonomic units. The sediments had significantly higher alpha diversity in crab ponds compared to that in fish and crayfish ponds. The fungal phyla largely belonged to Ascomycota and Chytridiomycota, and the dominance of Rozellomycota over Basidiomycota and Aphelidiomycota was observed. The majority of sediment fungal members were ascribed to unclassified fungi, with higher proportions in fish ponds than crab and crayfish ponds. Further, the fungal communities were markedly distinct among the three types of ponds, suggesting divergent patterns of fungal community assemblages caused by farming practices in aquaculture ponds. The community diversity and structure were closely correlated to sediment properties, especially sediment carbon content and pH. Thus, the distribution and pattern of fungal communities in the sediments appear to primarily depend on species-based farming practices responsible for the resulting sediment carbon content and pH in aquaculture ponds. This study provides a detailed snapshot and extension of understanding fungal community structure and variability in pond ecosystems, highlighting the impacts of farming practices on the assembly and succession of sediment fungal communities in aquaculture ponds.