Community Structure Of Bacteria Research Articles

Low soil carbon saturation deficit limits the abundance of cbbL-carrying bacteria under long-term no-tillage maize cultivation in northern China

The responses of cbbL-carrying bacteria to different levels of soil carbon saturation deficits (SCSD) under tillage managements are largely unknown. We assessed the influence of SCSD on the abundance and diversity of cbbL-carrying bacteria under long-term no-tillage with residue retention (NT) and conventional tillage without residue retention (CT) cultivation systems in maize. We found SCSD was smaller under NT than under CT in the 0–15 cm soil layer. The abundance and the Shannon diversity of cbbL-carrying bacteria in the NT treatment were lower than in the CT treatment. Soil carbon saturation and cbbL gene abundance showed a significant positive correlation, but there was no correlation between soil carbon saturation and cbbL gene diversity. However, the long-term NT practice decreased cbbL-carrying bacteria diversity and altered the community structure of the cbbL-carrying bacteria. Our results indicated that low SCSD limited the abundance of cbbL-carrying bacteria, but there was no relationship between low SCSD and diversity of cbbL-carrying bacteria. We suggest that further studies of cbbL-carrying bacteria carbon sequestration rates and capacity should be based on the effect of management practices on cbbL-carrying bacteria abundance and diversity. Our study has important implications for the relationship between the biological and physicochemical mechanisms in CO2 fixation.

Combined slag and biochar amendments to subtropical paddy soils lead to a short-term change of bacteria community structure and rise of soil organic carbon

Applying industrial waste amendments, such as steel slag and biochar, to soils is an increasingly common practice to improve soil fertility, crop yield, and soil carbon (C) pool storage and stability. However, the effects of separate and combined applications of slag and biochar on total and active soil organic C (SOC) pools and the associated relationships between soil microorganisms and C cycling are unclear. Therefore, this study examined the effects of steel slag, rice straw biochar, and slag+biochar amendments to subtropical early and late rice paddy soils on total and active SOC concentrations and microbial abundance and diversity. The results showed that slag+biochar increased SOC content in early and late rice, with increases in dissolved organic C of 28.7 and 52.6 % in the early and late rice jointing stages, respectively. Soil organic C was positively correlated with soil C:N ratios in the two crop seasons. Applications of slag and biochar alone increased the diversity of soil bacteria in early rice but decreased in late rice. Meanwhile, the combined application of slag and biochar decreased diversity of soil bacterial community diversity and increased the relative abundance of some beneficial bacterial taxa, such as Pseudomonas, Bacillus, Flavisolibacter, and Ferruginibacte which are related to SOC cycling and sequestration. The results highlight that the combined slag and biochar amendments can improve soil specific properties, such as pH and SOC stocks, which elicit alterations in soil bacterial composition, especially of some keystone genera, altogether resulting in enhanced soil C sequestration and C pool stability.

Differences in Bacterial Community Structure in Rhizosphere Soil of Three Caragana Species and Its Driving Factors in a Common Garden Experiment

The soil bacterial diversity and community structures in rhizosphere soil of Caragana microphylla, Caragana liouana, and Caragana roborovskyi in a common garden experiment were measured using the high-throughput sequencing technique, with the aim of investigating the factors driving the variation in the bacterial community structure. The results indicated that 42 phyla, 55 classes, 123 orders, 244 families, and 558 genera were obtained from the rhizosphere soil. The dominant phyla in all sample sites were Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes, Firmicutes, and Acidobacteria (relative abundance>1%). At the genus level, Phenylobacterium, Ensifer, and Chitinophaga were dominant. Two-way analysis of variance showed that species had a significant effect on the Shannon index and Simpson index of rhizosphere soil bacteria of the three Caragana species, whereas the Chao1 index, Shannon index, and Simpson index were significantly affected by the interaction of provenances and species. There was a significant difference among the three species in the composition of bacterial communities, and the cluster analysis indicated that the composition of the soil bacterial community significantly differed among provenances in C. liouana and C. roborovskyi. Based on the redundancy analysis, mean annual precipitation and altitude were the dominant factors influencing the rhizosphere soil bacterial community structure. Overall, the present results indicated that there were intraspecific and interspecific differences in the diversity and community structures of rhizosphere soil bacteria, and the bacterial community structure was mainly affected by the provenance climate. These results provide a theoretical basis for understanding the adaptation strategies and ecological restoration of the three Caragana species.

Community structure of aerobic anoxygenic phototrophic bacteria in algae- and macrophyte-dominated areas in Taihu Lake, China

Community structure of aerobic anoxygenic phototrophic bacteria in algae- and macrophyte-dominated areas in Taihu Lake, China

Responses of Bacterial Communities in Soils under Winter Wheat to Nightly Warming and Nitrogen Addition

Understanding soil bacterial diversity under global warming is necessary because of its crucial role in soil nitrogen cycling. However, the interaction effect of warmer temperatures and nitrogen application on bacterial communities in the soils of winter wheat fields is unclear. In this study, the air temperature was increased with infrared heating, and this heating treatment was combined with nitrogen fertilizer application. The two-year continuous temperature increase significantly decreased the soil’s pH and nitrate nitrogen content, but significantly increased the content of soil available nutrients. Warming changed the community structure of the soil bacteria, and significantly increased the bacterial richness and diversity by 17.77% and 3.52%, respectively. The changes in the physical and chemical properties of the soil caused by the increased nighttime temperature decreased the percentage abundance of Pseudomonadota, which is the largest bacterial phylum, and plays an important role in the global carbon, sulfur, and nitrogen cycles. The structural equation model demonstrated that the influence of soil temperature on bacterial diversity was mediated through soil moisture. Nitrogen application rate directly affected soil bacterial diversity and was the most significant parameter influencing bacterial diversity.

Community structure and co-occurrence network analysis of bacteria and fungi in wheat fields vs fruit orchards.

Soil microorganisms play a vital role in biogeochemical processes and nutrient turnover in agricultural ecosystems. However, the information on how the structure and co-occurrence patterns of microbial communities response to the change of planting methods is still limited. In this study, a total of 34 soil samples were collected from 17 different fields of 2 planting types (wheat and orchards) along the Taige Canal in Yangtze River Delta. The structure of bacterial and fungal communities in soil were determined by 16S rRNA gene and ITS gene, respectively. The dominated bacteria were Proteobacteria, Acidobacteriota, Actinobacteriota, Chloroflexi, Bacteroidota, and Firmicutes. The relative abundances of Actinobacteriota and Firmicutes were higher in the orchards, while Chloroflexi and Nitrospirota were more abundant in wheat fields. Ascomycota, Mortierellomycota, and Basidiomycota were the predominant fungus in both soil types. Diversity of bacterial and fungal communities were greater in the wheat fields than in orchards. Statistical analyses showed that pH was the main factor shaping the community structure, and parameters of water content (WC), total organic carbon (TOC) and total nitrogen (TN) had great influences on community structure. Moreover, high co-occurrence patterns of bacterial and fungal were confirmed in both wheat fields and orchards. Network analyses showed that both wheat fields and orchards occurred modular structure, including nodes of Acidobacteriota, Chloroflexi, Gemmatimonadota, Nitrospirota and Ascomycota. In summary, our work showed the co-occurrence network and the convergence/divergence of microbial community structure in wheat fields and orchards, giving a comprehensive understanding of the microbe-microbe interaction during planting methods' changes.

Chlorella potential to purify domestic garbage leachate for biomass production and community structure responses of wastewater-borne bacteria

The microalgae growth, accumulation of high value-added substances of Chlorella sp. HQ and its water purification potential during cultivation in diluted domestic garbage leachate (DGL) were investigated and changes in the structure of wastewater-borne bacteria community were also analyzed. Results showed that the highest density of Chlorella (1.70 × 108 cells/mL) was obtained in DGL diluted 5 times with rural sewage, the contents of protein and sugar in microalgae cells were 36.0 % and 45.6 %, Moreover, energy volumetric yield reached 48.54 kJ/L. After 15 d of microalgae treatment, the removal rates of total nitrogen (TN), ammonia nitrogen (NH4+-N), chemical oxygen demand (COD), total phosphorus (TP) of diluted DGL were 88.2 %, 97.3 %, 94.9 %, and 95.2 %, respectively, with the fluorescence peaks of humic-like organic matter shifting to longer wavelengths. Moreover, high-throughput sequencing of wastewater-borne bacteria showed that microalgae growth could promote the enrichment of denitrifying polyphosphate accumulating bacteria, which suggests that wastewater-borne bacteria and Chlorella may form a cooperative mode to achieve water purification.

Effects of Nitrogen Addition on Soil Carbon-Fixing Microbial Diversity on Different Slopes in a Degraded Alpine Meadow.

Autotrophic carbon-fixing bacteria are a major driver of carbon sequestration and elemental cycling in grassland ecosystems. The characteristics of the response of carbon-fixing bacterial communities to nitrogen (N) addition in degraded alpine meadows are unclear. In this study, it was investigated that the effects of N addition in three levels [they are low (LN), middle (MN), and high (HN) with N supplement of 2, 5, and 10 g N⋅m–2⋅a–1, respectively] on soil carbon-fixing bacteria on different slopes in a degraded alpine meadow in the Yellow River on the Qinghai–Tibet Plateau. The results showed that there were significant differences in the abundance of some low abundance genera of carbon-fixing bacteria on the same slope (P < 0.05), but the differences in the abundance of various phyla and dominant genera were not significant. MN on gentle slopes significantly reduced the Chao1 index and observed species (P < 0.05), whereas N addition on steep slopes had no significant effect on the diversity. The abundance of the Cyanobacteria phylum and 28 genera of identified carbon-fixing bacteria differed significantly between slopes (P < 0.05), and observed species of carbon-fixing bacteria were significantly higher on steep slopes than on gentle slopes (P < 0.05). Factors affecting the carbon-fixing bacteria community structure include slope, N addition, ammoniacal nitrogen (N-NH4+), microbial biomass carbon (MBC), soil water content (SWC), pH, soil C:N ratio, and microbial C:N ratio. Slope, N addition, soil physicochemical properties, microbial biomass, and stoichiometric ratio did not significantly affect the carbon-fixing bacteria diversity. Thus, the effect of exogenous N addition on carbon-fixing bacteria in degraded alpine meadows was dependent on slope conditions, and the response of carbon-fixing bacteria abundance and species number to N addition on gently slope sites was threshold-limited.

Impacts of near‐natural management in eucalyptus plantations on soil bacterial community assembly and function related to nitrogen cycling

Abstract Eucalyptus trees have been widely planted in China as commercial timber, which has caused severe soil erosion and water deficiency. Near‐natural management by mixing eucalyptus with nitrogen‐fixing tree species has been used in plantations to alleviate these problems. In the present study, we investigated the changes in soil microbial community and function in eucalyptus plantations mixed with nitrogen‐fixing trees and with different rotation histories (first and second generation) using Illumina MiSeq. of 16S rRNA gene, coupled with Functional Annotation of Prokaryotic Taxa (FAPROTAX) and Quantitative Microbial Element Cycling (QMEC) analyses. Both management systems (mixed with nitrogen‐fixing trees and with different rotating time) increased the soil bacterial α‐diversity. The plantations with different management histories formed different bacterial communities and potential functional structures. Mixing with nitrogen‐fixing trees increased the abundance of Actinobacteria involved in the nitrogen cycle and the abundance of K‐strategy bacteria (Acidobacteria, Verrucomicrobia, Chloroflexi) in both first‐ and second‐generation plantations. Functionally, the expression of nitrogen‐fixing (nifH) and nitrification genes (amoA1 and hao) increased and that of denitrification genes (nirk2, nirk3, nirS1 and nosZ2) decreased in plantations mixed with nitrogen‐fixing trees. The soil pH, soil water content and bacterial biomass were the key factors driving bacteria community and functional structures. The strategy of mixing eucalyptus with nitrogen‐fixing trees can increase the efficiency of nitrogen cycling by accelerating the nitrogen‐fixing and nitrifying process while inhibiting the denitrifying process. The results highlight the importance of mixing eucalyptus with nitrogen‐fixing trees for soil microbes and provide useful information on the management of eucalyptus plantations in the future. Read the free Plain Language Summary for this article on the Journal blog.

Distinct Patterns of Rhizosphere Microbiota Associated With Rice Genotypes Differing in Aluminum Tolerance in an Acid Sulfate Soil.

Rhizosphere microbes are important for plant tolerance to various soil stresses. Rice is the most aluminum (Al)-tolerant small grain cereal crop species, but the link between rice Al tolerance and rhizosphere microbiota remains unclear. This study aimed to investigate the microbial community structure of aluminum-sensitive and Al-tolerant rice varieties in acid sulfate soil under liming and non-liming conditions. We analyzed the rice biomass and mineral element contents of rice plants as well as the chemical properties and microbial (archaea, bacteria, and fungi) communities of rhizosphere and bulk soil samples. The results showed that the Al-tolerant rice genotype grew better and was able to take up more phosphorus from the acid sulfate soil than the Al-sensitive genotype. Liming was the main factor altering the microbial diversity and community structure, followed by rhizosphere effects. In the absence of liming effects, the rice genotypes shifted the community structure of bacteria and fungi, which accounted for the observed variation in the rice biomass. The Al-tolerant rice genotype recruited specific bacterial and fungal taxa (Bacillus, Pseudomonas, Aspergillus, and Rhizopus) associated with phosphorus solubilization and plant growth promotion. The soil microbial co-occurrence network of the Al-tolerant rice genotype was more complex than that of the Al-sensitive rice genotype. In conclusion, the bacterial and fungal community in the rhizosphere has genotype-dependent effects on rice Al tolerance. Aluminum-tolerant rice genotypes recruit specific microbial taxa, especially phosphorus-solubilizing microorganisms, and are associated with complex microbial co-occurrence networks, which may enhance rice growth in acid sulfate soil.

Cyperus rotundus L. drives arable soil infertile by changing the structure of soil bacteria in the rhizosphere, using a maize field as an example

Rhizosphere microorganisms can greatly affect plant growth, especially the plant growth-promoting rhizobacteria (PGPR), which can improve plant root development and growth because they contain various biological functions including nitrogen fixation, phosphate solubilization, and phytosiderophore production. This study demonstrates that Cyperus rotundus L. is capable of developing and forming complex underground reproductive systems at arbitrary burial depths and cutting modes due to its extremely strong multiplication and regeneration ability. With the densities of C. rotundus increasing, the abundance of PGPR, soil enzymes invertase and urease, the nutrient contents of the field soil, and maize quality were impacted. Notably, more abundance of PGPR-most notably, the nitrogen-fixing microorganisms (NFMs) such as Azospirillum, Burkholderia, Mycobacterium, and Rhizobium-enriches in the rhizosphere of C. rotundus than in that of maize. In addition, the activities of soil enzymes invertase (S_SC) and urease (S_SU) were significantly higher in its rhizosphere than in maize, further proving that more NFMs enrich the C. rotundus rhizosphere. The nutrient contents of the field soil of TN, SOM, and SOC were reduced, indicating that the presence of C. rotundus made the soil infertile. Hence, these pieces of evidence indicate that C. rotundus may drive the field soil infertile as reflected by reduced soil nutrients via altering rhizosphere bacteria community structure.

Diversity patterns and drivers of soil bacterial and fungal communities along elevational gradients in the Southern Himalayas, China

Elucidating the diversity patterns and drivers of soil microbes at high altitudes contributes to understanding the role microbes play in ecosystem services, but little is known about the soil microbial diversity, richness and abundance patterns across elevations on the Tibetan Plateau. This study was conducted to explore the shifts of forest soil bacterial and fungal community diversities and the regulating factors along an elevation gradient (2980–4050 m a.s.l.) in the Southern Himalayas of China. Illumina sequencing of 16S rRNA and ITS1, and quantitative real-time PCR were used to determine soil bacterial and fungal communities, coupled with plant diversity survey and edaphic properties analysis. The results revealed that plant alpha-diversity reached the highest level at an elevation of 3255 m and subsequently decreased with higher elevations; while soil bacterial alpha-diversity and fungal richness reached the lowest at 3590 m and 3772 m respectively, then increased with higher elevations; soil microbial abundance decreased with increasing elevation. The soil pH was the main driver of the elevation-related soil bacterial richness, diversity, and abundance. Soil nutrients contributed most to the fungal richness, diversity, and abundance. The total phosphorus content was the optimal predictor of fungal richness and abundance, while nitrate levels determined the fungal diversity. The community structures of bacteria and fungi differed significantly among elevations (Pbacteria = 0.001, Pfungi = 0.001). The elevation and edaphic properties (including the contents of soil organic matter and pH) controlled the elevation patterns of soil bacterial community structures and explained 56.1 % of the total variation. In contrast, edaphic properties (including SOC, TP and pH) primarily shaped the elevation patterns of soil fungal community structures and explained 38.7 % of the total variation. This study provides comprehensive insights into soil microbial geography associated with the biogeochemical cycling on the Tibetan Plateau.

Antibiotic-Induced Treatments Reveal Stress-Responsive Gene Expression in the Endangered Lichen Lobaria pulmonaria

Antibiotics are primarily found in the environment due to human activity, which has been reported to influence the structure of biotic communities and the ecological functions of soil and water ecosystems. Nonetheless, their effects in other terrestrial ecosystems have not been well studied. As a result of oxidative stress in organisms exposed to high levels of antibiotics, genotoxicity can lead to DNA damage and, potentially, cell death. In addition, in symbiotic organisms, removal of the associated microbiome by antibiotic treatment has been observed to have a big impact on the host, e.g., corals. The lung lichen Lobaria pulmonaria has more than 800 associated bacterial species, a microbiome which has been hypothesized to increase the lichen’s fitness. We artificially exposed samples of L. pulmonaria to antibiotics and a stepwise temperature increase to determine the relative effects of antibiotic treatments vs. temperature on the mycobiont and photobiont gene expression and the viability and on the community structure of the lichen-associated bacteria. We found that the mycobiont and photobiont highly reacted to different antibiotics, independently of temperature exposure. We did not find major differences in bacterial community composition or alpha diversity between antibiotic treatments and controls. For these reasons, the upregulation of stress-related genes in antibiotic-treated samples could be caused by genotoxicity in L. pulmonaria and its photobiont caused by exposure to antibiotics, and the observed stress responses are reactions of the symbiotic partners to reduce damage to their cells. Our study is of great interest for the community of researchers studying symbiotic organisms as it represents one of the first steps to understanding gene expression in an endangered lichen in response to exposure to toxic environments, along with dynamics in its associated bacterial communities.

Potential role of nitrite-dependent anaerobic methane oxidation in methane consumption and nitrogen removal in Chinese paddy fields

Nitrite-dependent anaerobic methane oxidation (n-damo), catalyzed by bacteria closely related to Candidatus Methylomirabilis oxyfera, links the global carbon and nitrogen cycles. Currently, the contribution of n-damo in controlling methane emissions and nitrogen removal, and the key regulatory factors of this process in Chinese paddy fields are poorly known. Here, soil samples from 20 paddy fields located in different climate zones across China were collected to examine the n-damo activity and bacterial communities. The n-damo activity and bacterial abundance varied from 1.05 to 5.97 nmol CH4 g−1 (dry soil) d−1 and 2.59 × 105 to 2.50 × 107 copies g−1 dry soil, respectively. Based on the n-damo activity, it was estimated that approximately 0.91 Tg CH4 and 2.17 Tg N could be consumed annually via n-damo in Chinese paddy soils. The spatial variations in n-damo activity and community structure of n-damo bacteria were significantly (p < 0.05) affected by the soil ammonium content, labile organic carbon content and pH. Furthermore, significant differences in n-damo activity, bacterial abundance and community composition were observed among different climate zones. The n-damo activity was found to be positively correlated with the mean annual air temperature. Taken together, our results demonstrated the potential importance of n-damo in both methane consumption and nitrogen removal in Chinese paddy soils, and this process was regulated by local soil and climatic factors.

Bacterial Community Structure and Potential Microbial Coexistence Mechanism Associated with Three Halophytes Adapting to the Extremely Hypersaline Environment.

Halophytes play a crucial ecological role in drought and saline–alkali environments. However, there is limited knowledge about the structure of bacterial communities and the potential microbial coexistence mechanism associated with halophytes. This study investigated the diversity and community structure of endophytic and rhizospheric bacteria associated with three halophytes by applying high-throughput sequencing and geochemistry analyses on the studied soils. We collected 18 plant and 21 soil samples, and sequenced the V3 and V4 hypervariable regions of the 16S rRNA gene using next-generation sequencing (NGS). We also assessed geochemistry of the studied soils. The research suggested that rhizospheric bacterial richness and diversity associated with three halophytes were all significantly higher than for endophytic bacteria. The microbial community analysis indicated that Actinobacteria, Firmicutes, Bacteroidetes and Proteobacteria were the dominating bacterial phyla. Most unassigned operational taxonomic units (OTUs) implied that the microbes associated with halophytes contained abundant potential novel taxa, which are significant microbial resources. The high-abundance OTU phylogenetic tree supported the above views as well. Additionally, network analysis indicated that some conditional rare taxa (CRT) also might be keystone taxa during halophyte microbial community construction. The results of non-metric multidimensional scaling (NMDS) ordination analysis indicated significant dissimilarities in the microbial community among different sample groups. Sixty-two biomarkers were detected from seven different sample groups by linear discriminant analysis effect size (LEFSe) analysis. Microbial functions predicted based on phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt2) demonstrated that the abundances of nitrogen metabolism genes of endophytic bacteria were significantly higher than in rhizobacteria. Environmental factor analysis confirmed that different soil properties have different degrees of influence on the abundance and composition of the microbiota. To better adapt to the extreme hypersaline environment, halophytes could specifically recruit some plant beneficial bacterial taxa, such as nitrogen-fixing bacteria and extremely halophilic or halotolerant bacteria, to help them robustly grow and proliferate. All our preliminary results highlight microbial diversity and community related to halophytes grown on saline–alkali land of arid areas. Simultaneously, this work also advanced our further understanding of the halophyte microbiome associated with plants, and their role in plant adaptation to the extremely hypersaline environment.

Distinct Elevational Patterns and Their Linkages of Soil Bacteria and Plant Community in An Alpine Meadow of the Qinghai-Tibetan Plateau.

Soil microbes play important roles in determining plant community composition and terrestrial ecosystem functions, as well as the direction and extent of terrestrial ecosystem feedback to environmental changes. Understanding the distribution patterns of plant and soil microbiota along elevation gradients is necessary to shed light on important ecosystem functions. In this study, soil bacteria along an elevation gradient in an alpine meadow ecosystem of the Qinghai–Tibetan Plateau were investigated using Illumina sequencing and GeoChip technologies. The community structure of the soil bacteria and plants presented a continuous trend along the elevation gradient, and their alpha diversity displayed different distribution patterns; however, there were no linkages between them. Beta diversity of the soil bacteria and plants was significantly influenced by elevational distance changes (p < 0.05). Functional gene categories involved in nitrogen and phosphorus cycling had faster changes than those involved in carbon degradation, and functional genes involved in labile carbon degradation also had faster variations than those involved in recalcitrant carbon degradation with elevational changes. According to Pearson’s correlation, partial Mantel test analysis, and canonical correspondence analysis, soil pH and mean annual precipitation were important environmental variables in influencing soil bacterial diversity. Soil bacterial diversity and plant diversity had different distribution patterns along the elevation gradient.

Composition and key-influencing factors of bacterial communities active in sulfur cycling of soda lake sediments.

Bacteria are important participants in sulfur cycle of the extremely haloalkaline environment, e.g. soda lake. The effects of physicochemical factors on the composition of sulfide-oxidizing bacteria (SOB) and sulfate-reducing bacteria (SRB) in soda lake have remained elusive. Here, we surveyed the community structure of total bacteria, SOB and SRB based on 16S rRNA, soxB and dsrB gene sequencing, respectively, in five soda lakes with different physicochemical factors. The results showed that the dominant bacteria belonged to the phyla Proteobacteria, Bacteroidetes, Halanaerobiaeota, Firmicutes and Actinobacteria. SOB and SRB were widely distributed in lakes with different physicochemical characteristics, and the community composition were different. In general, salinity and inorganic nitrogen sources (NH4+-N, NO3--N) were the most significant factors. Specifically, the communities of SOB, mainly including Thioalkalivibrio, Burkholderia, Paracoccus, Bradyrhizobium, and Hydrogenophaga genera, were remarkably influenced by the levels of NH4+-N and salinity. Yet, for SRB communities, including Desulfurivibrio, Candidatus Electrothrix, Desulfonatronospira, Desulfonatronum, Desulfonatronovibrio, Desulfonatronobacter and so on, the most significant determinants were salinity and NO3--N. Besides, Rhodoplanes played a significant role in the interaction between SOB and SRB. From our results, the knowledge regarding the community structures of SOB and SRB in extremely haloalkaline environment was extended.

Diversity of indigenous bacteria in fermented dough with Saccharomyces cerevisiae Y10 and Torulaspora delbrueckii Y22

There is a great diversity of indigenous microorganisms in flour, the number of which increased greatly during long-term dough fermentation, affecting dough fermentation and product quality. In this study, the diversity of indigenous bacteria in fermented dough inoculated with single Saccharomyces cerevisiae Y10 strain, Torulaspora delbrueckii Y22 strain and their co-culture was revealed by Illumina MiSeq sequencing. Compared with the dough without yeast inoculation, the bacteria diversity in yeast fermented dough was lower after 12 h fermentation. However, the abundance of lactic acid bacteria (LAB) in the dough inoculated with yeast was higher than that in dough without any yeast inoculated. Similar community structures of bacteria were found in doughs inoculated with different yeast, but their abundance were different. The abundance of the genus Clostridium in doughs inoculated with single S. cerevisiae Y10 was lower than non-inoculated dough, doughs inoculated with T. delbrueckii Y22 and co-culture of S. cerevisiae Y10 and T. delbrueckii Y22 at the same fermentation stage. In comparison with the dough without yeast inoculation, the presence of T. delbrueckii Y22 and the co-culture of S. cerevisiae Y10 and T. delbrueckii Y22 decreased the relative abundance of Staphylococcus, Cronobacter and Enterobacter in fermented dough. Furthermore, the relative abundance of Komagataeibacter increased in the presence of co-culture of S. cerevisiae Y10 and T. delbrueckii Y22. The results of this study suggested that the diversity of indigenous bacteria during dough fermentation was greatly influenced by the starter strain.

Inoculation with Penicillium citrinum aids ginseng in resisting Fusarium oxysporum by regulating the root and rhizosphere microbial communities

Ginseng root rot disease caused by Fusarium oxysporum severely decreases root yield and quality, causing huge economic losses. Biological control is safe, environmentally friendly and sustainable. The results from bananas, sunflowers and chickpeas showed that Penicillium citrinum could control root diseases. However, its potential to control root rot disease of the medicinal plant is unclear. Here, the effects of P. citrinum YW322 isolated from ginseng rhizosphere soil on controlling root rot disease of ginseng were evaluated using the pot experiment. Four treatments were set up: no inoculation (CK), P. citrinum inoculation (PC), F. oxysporum inoculation (FO) and mixed inoculation of P. citrinum and F. oxysporum (PCFO). The results showed that the PC treatment did not affect ginseng growth when compared with the CK treatment. The plants in FO grew more slowly and rotted more severely. Distinct from FO, the ginseng plants in the PCFO treatment all grew similarly to CK. Plate confrontation experiments showed that P. citrinum YW322 inhibited the mycelium growth of F. oxysporum YFW32 by 95.75%. After 7 days of cultivation, the filtrate secreted nonvolatile inhibitory substances with 58.82% inhibition. The results from high-throughput sequencing showed that the structure of the bacterial community in ginseng roots and the fungal community in rhizosphere soil in the PCFO treatment were significantly different compared to the FO treatment (p < 0.05). Compared with FO, the abundance of Clostridium was significantly suppressed in the ginseng roots of PCFO treatment (93.5% reduction) (p < 0.05); significant enrichment of fungi such as Mortierella, Trichoderma and Penicillium was observed in ginseng rhizosphere soil in the PCFO treatment (8.26%, 17.44% and 2.80% increase in relative abundance, respectively). The relative abundance of the pathogenic fungus Fusarium decreased 31.85% compared with FO (p < 0.05). Soil physicochemical analysis showed that compared to the FO treatment, the soil pH and S-CAT activity in the PCFO treatment significantly increased (p < 0.05). Therefore, P. citrinum has potential to control ginseng root rot disease by directly inhibiting the growth of F. oxysporum and regulating the community structure of root bacteria and rhizosphere fungi to help ginseng resist F. oxysporum.

Bacterial Community Composition and Function in a Tropical Municipal Wastewater Treatment Plant

Bacterial diversity and community composition are of great importance in wastewater treatment; however, little is known about the diversity and community structure of bacteria in tropical municipal wastewater treatment plants (WWTPs). Therefore, in this study, activated sludge samples were collected from the return sludge, anaerobic sludge, anoxic sludge, and aerobic sludge of an A2O WWTP in Haikou, China. Illumina MiSeq high-throughput sequencing was used to examine the 16S ribosomal RNA (rRNA) of bacteria in the samples. The microbial community diversity in this tropical WWTP was higher than in temperate, subtropical, and plateau WWTPs. Proteobacteria, Bacteroidota, Patescibacteria, and Chloroflexi were the dominant phyla. Nitrification bacteria Nitrosomonas, and Nitrospira were also detected. Tetrasphaera, instead of Candidatus Accumulibacter, were the dominant polyphosphate accumulating organisms (PAOs), while, glycogen accumulating organisms (GAOs), such as Candidatus Competibacter and Defluviicoccus were also detected. The bacterial community functions predicted by PICRUSt2 were related to metabolism, genetic information processing, and environmental information processing. This study provides a reference for the optimization of tropical municipal WWTPs.