Abundance Of Fungal Communities Research Articles

Microbial community dynamics during the storage of industrial-scale wood chip piles of Picea abies and Populus canadensis and the impact of an alkaline stabilization agent

Storage of woody biomass in large wood chip piles is unavoidable for biotechnological applications, but comes along with considerable biomass-, energy- and thus, economic losses due to exothermic reactions and microbial degradation. The homogeneous amendment of the storage piles with an alkaline stabilization agent, calcium hydroxide (Ca(OH)2), was found to decrease dry matter loss in Picea abies; for Populus canadensis piles the effects cannot clearly be deduced. Here we investigated the bacterial and fungal communities of industrial-scale wood chip piles (250 m3) of these two different tree species and related them to physicochemical conditions and enzymatic activities after 35 and 120 d, representing short- and long-term storage of the wood chips, respectively. Coming from different wood types (hard vs. softwood), we expected the communities to converge over time, due to similar storage conditions. Despite pH posing selective pressure, we expected a minor Ca(OH)2 effect as already known from previous studies.We found that the effectiveness of Ca(OH)2 addition depended on the wood type that determined both the native microbial seeding community and temperature pattern of all piles, thereby exerting selective forces of differing strength. Generally, a thermophilic community consisting of single fungal and variable bacterial taxa were identified. As expected, the microbial communities from P. abies and P. canadensis converged over time. Biomass loss was connected to C-cycle related enzymatic activities and to the abundance and composition of fungal communities. Chaetomium sp. was identified as potential key taxon determining biomass degradation under the given storage conditions.

Effects of Land Conversion on Soil Microbial Community Structure and Diversity in Songnen Plain, Northeast China

To feed the growing human population, natural grasslands are being converted to agricultural use at a massive scale. This conversion may have consequences for soil biodiversity, but its impact on the community assembly of differentially microbial groups remains largely unknown. Here, we selected the three typical land-use types: grassland, arable land (formerly grassland), and forest (formerly grassland) in the Songnen Plain, Northeastern China. Illumina MiSeq high-throughput sequencing technology based on bacterial 16S rRNA and fungal ITS rRNA was used to study the community structures and diversities of soil bacteria and fungi and to explore the drivers of these changes. The results showed that bacterial community diversity did not change after grassland conversion to forest and arable land, but affected bacterial community abundance at the phylum level. Actinomycetes and Proteobacteria were significantly reduced, Acidobacteria were significantly increased, and Gemmatimonadetes and Bacteroidetes were the most abundant in arable land. Land conversion had significant effects on both fungal community diversity and abundance. After the grassland was converted into forest, the fungal community diversity decreased, but the community abundance increased significantly, the Ascomycetes decreased significantly, and Basidiomycetes became the dominant phylum, especially white rot fungi. Interestingly, the fungal community diversity and community abundance increased significantly after grassland was converted to arable land, and the abundance of Zygomycota increased significantly but the dominant phylum was still Ascomycetes. Canonical correlation analysis (CCA) showed pH, MC, NO3−-N, TP, AP, and other soil factors are important factors affecting the composition of microbial communities. In the soil of this study area, the composition of bacterial communities is mainly driven by changes in pH and soil texture, and the composition of fungal communities is most closely related to changes in soil nutrient utilization. Changes in land-use patterns have an effect on the structure and diversity of microbial communities by changing the physical and chemical properties of the soil.

Great gerbil burrowing-induced microbial diversity shapes the rhizosphere soil microenvironments of Haloxylon ammodendron in temperate deserts

In the Gurbantunggut Desert of northwest China, the main habitat of Rhombomys opimus (great gerbil) is under the thickets of Haloxylon ammodendron, the main construction species. In the long-term coexistence, continuous gerbil activities (burrowing, defecating, and gnawing) limited the growth of H. ammodendron, affected the root microenvironment under the H. ammodendron forest, and weakened the desert ecosystem. However, there is a lack of general understanding about the response of desert soil microhabitats to such gerbil disturbance. Accordingly, this study examined the effects of different intensities of gerbil disturbance (none, mild, moderate, or severe disturbances) on soil nutrients content and used high-throughput sequencing to explore the change in diversity and structure of microbial communities (bacteria and fungi) in H. ammodendron rhizosphere at different soil depths (0–20, 20–40, and 40–60 cm). In the arid desert ecosystem, compared with the soil fungal community, the alpha diversity of the soil bacterial community was significantly affected by gerbil disturbance. Meanwhile, both soil depth and gerbil disturbance significantly impacted the beta diversity and relative abundance of soil bacterial and fungal communities. In addition, gerbil disturbance significantly altered the soil characteristics affecting the distribution and composition of soil microbial communities in H. ammodendron rhizosphere, especially the soil bacterial community. This survey provides evidence that remold impact of gerbil disturbance on soil microenvironment of H. ammodendron rhizosphere in desert ecosystems in northwest China, which helps to further understand the potential correlations with changes in the microbial community at a regional scale.

Development of a soil quality index for sequences with different levels of land occupation using soil chemical, physical and microbiological properties

The sustainable intensification of agricultural systems through crop rotations and/or the use of winter service crops can contribute to the diversification of the systems. This alteration of the surface layer creates conditions that favor an increase in the diversity of soil microbial communities, which improves the recovery capacity of the edaphic system, thereby contributing beneficial effects to plants, soil, and ecosystem. Our objectives were: 1) to evaluate the effect of crops sequences on soil chemical, physical and microbial parameters, and 2) to develop a soil quality index (SQI) from a minimum set of indicators for cropping sequences with different levels of land occupation. A long field experiment under no-tillage was established in 2006, where soil samples were collected during three agricultural seasons (2015, 2016, and 2017). We compared the effects of four different crop sequences that included soybean (S), maize (M) and wheat (W), and also incorporated wheat as a winter cover crop (CC), being S-S, CC/S, M-W/S, and W/S-CC/M. We found that sustainable management practices, crop rotation and inclusion of CC increased soil organic carbon. The highest basic infiltration rate and lowest penetration resistance values were found for double-cropped wheat/soybean-winter cover crop/maize (W/S-CC/M), the most intensified sequence. The average microbial biomass carbon level for soybean monoculture, was reduced by 32 % compared to maize-double-cropped wheat/soybean in the three agricultural seasons, while the metabolic coefficient in soybean monoculture and winter cover crop/soybean was significantly higher. In soybean monoculture, hydrolysis of fluorescein diacetate was decreased by 28.5 %, while dehydrogenase activity was increased by 43 % with respect to double-cropped wheat/soybean-winter cover crop/maize. The abundance of fungal and bacterial communities did not reveal significant variations between sequences by quantitative PCR analysis. The SQI was constructed by selecting a minimum set of indicators based on soil chemical, physical and microbial parameters. The parameters selected by the model were soil organic carbon, total organic nitrogen, basic infiltration rate, microbial respiration and hydrolysis of fluorescein diacetate, that revealed the differences among crop sequences in response to land occupation. The inclusion of different crops increased the SQI in comparison with soybean monoculture. The double-cropped wheat/soybean-winter cover crop/maize system improved the SQI by 73 % compared to soybean monoculture. Our findings show that crop sequences with high soil occupation improved their chemical and physical properties, as well as increasing the abundance and functionality of the microbial community, which is related to a better SQI.

Mechanism underlying the response of fungi and their Fusarium symbiotic networks to the rotations of soybean and corn

Fusarium oxysporum and Fusarium solani are the main soybean root rot pathogens in northern China. We investigated the distribution and driving factors of Fusarium under different cropping systems to evaluate and regulate soil health. The factors affecting Fusarium in soybean cropping systems were assessed using high-throughput sequencing of ITS1 to identify soil microbial population diversity, and then the soil physicochemical properties were assessed to determine the levels of various elements present in the environment. According to the results, the abundance of Fusarium was obviously reduced in the corn–soybean rotation and uncultivated soil systems. The relative abundance of Fusarium in the soil and the abundance and diversity of fungal communities were significantly positively associated with the abundance of Ascomycota. Additionally, the relative abundance of Fusarium was significantly positively correlated with the zinc (Zn) content. When the Zn content was high, the abundance of Fusarium increased, and the correlations with Chaetomium, Cryptococcus, Penicillium and Trichoderma significantly decreased. Soybean yield was significantly negatively correlated with fungal community abundance and diversity. Based on our results, the uncultivated soil and corn–soybean rotation cropping systems improved the organizational structure of the soil fungal community and were conducive to the health and production of soybean.

Changes in Fungal and Oomycete Community Composition Following Irrigation Reductions Aimed at Increasing Water Use Efficiency in a Containerized Nursery Crop

Ornamental production in the United States spans an estimated 267,000 ha and uses approximately 169,000 m3 of water yearly. Ornamental growers, particularly those with air-closed systems, are interested in implementing reduced irrigation technologies such as sensor-controlled irrigation systems to improve water use efficiency in response to water scarcity. To evaluate phytobiome impacts, we utilized an Illumina metabarcoding approach to characterize changes in fungal and oomycete rhizosphere communities of commercially grown poinsettia, complementing previous studies of single-pathogen impacts. Minor reductions (from 54 to 50% volumetric water content [VWC]) did not have large effects on rhizosphere fungal community structure but shifts in plant health status (symptomatic to asymptomatic) correlated with shifts in fungal diversity and evenness, with an increased abundance of several taxa, including Plectosphaerella cucumerina and Fusarium spp., in symptomatic plants. Further reductions in irrigation (45, 35, and 25% VWC) did not affect overall fungal community composition but the lowest VWC increased the abundance of potential root rot pathogens such as Phoma multirostrata and Plectosphaerella cucumerina. Reduced irrigation volumes decreased oomycete diversity and abundance of several known pathogens in the Phytophthora genus. Addition of a bacterial product (Companion) with putative pathogen-suppressive and drought-tolerance enhancing effects had no influence on fungal community composition or abundance but did increase abundance of some oomycete species at 45% VWC. This study shows that adoption of reduced irrigation may have greater effects on fungal versus oomycete taxa in the system, with consistent patterns of fungal enhancement, including putative fungal pathogens and beneficial organisms, and oomycete suppression.

Effects of planting of two common crops, Allium fistulosum and Brassica napus, on soil properties and microbial communities of ginseng cultivation in northeast China

BackgroundLong-term cultivation of ginseng can cause severe crop disorders and soil sickness. Crop rotation is an effective agricultural management measure to improve soil sustainability and decrease pathogens. However, the suitable ginseng rotation system and the changes in soil microbial community and soil characteristics under the rotation system need to be further explored.MethodsTo explore suitable ginseng crop rotation systems and improve soil utilization, Allium fistulosum and Brassica napus were planted on ginseng cultivation soil for one year. The effects of the two crops on the chemical properties and enzyme activities of the ginseng cultivation soil were evaluated by chemical analysis. In addition, amplicon sequencing targeting 16 s rDNA genes of bacteria and ITS of fungi has been used to characterize the functional and compositional diversity of microbial communities.ResultsThe results elucidated that the levels of available phosphorus (AP) and available potassium (AK) in the soil increased significantly after one year of cultivation for both crops and Allium fistulosum cultivation may also have reduced soil salinity. In addition, the effects of the two crops on the activities of key soil enzymes were different. Catalase (CAT), urease (URE), and acid phosphatase (A-PHO) activities were significantly reduced and sucrase (SUC), and laccase (LAC) activities were significantly increased after Allium fistulosum planting. While A-PHO activity was significantly increased and LAC activity was significantly decreased after Brassica napus planting. Allium fistulosum significantly reduced the abundance of soil fungal communities. The cultivation of Allium fistulosum and Brassica napus significantly altered the composition of soil bacterial and fungal communities, where changes in the abundance of dominant microorganisms, such as Ascomycota, and Mortierellomycota, etc., were closely related to soil chemistry and enzyme activity. Moreover, both significantly reduced the abundance of the pathogenic fungus Ilyonectria.ConclusionsOur study clarified the effects of Allium fistulosum and Brassica napus on the microbial community and physicochemical properties of ginseng cultivated soil and provides a basis for the sustainable application of ginseng cultivation soil and the development of ginseng crop rotation systems.

Effects of Biodegradation of Corn-Starch-Sodium-Alginate-Based Liquid Mulch Film on Soil Microbial Functions.

In response to the problems of the poor degradability and mechanical properties of liquid mulch, natural non-toxic polymer compound corn starch and sodium alginate were used to prepare fully biodegradable liquid mulch. The preparation conditions of the mulch were optimized, and the mechanical properties of the mulch and the changes in the microbial community in soil with the mulch degradation were analyzed. The corn-starch–sodium-alginate-based liquid mulch film had an optimum performance at a tensile strength of 0.145 MPa and an elongation at a break of 16.05%, which was attained by adding 33.33% sodium alginate, 50% glycerol 22 and 4% citric acid to corn starch after moist heat modification. Fourier transform infrared spectroscopy analysis showed that the -COOH in sodium alginate could interact with the -OH in starch and glycerol through hydrogen bonding, thus, resulting in a denser structure and better mechanical properties of the liquid mulch as a non-crystalline material. The soil burial degradation study of mulch revealed that corn-starch–sodium-alginate-based liquid mulch degraded completely at 25 days macroscopically, and mulch degradation increased soil organic matter content. Microbial kinetic analysis showed that the abundance and diversity of the bacterial community decreased with the degradation of the mulch, which was conducive to the optimization of the bacterial community structure and function. Arthrobacter of the class Actinomycetes became the dominant microorganism, and its abundance increased by 16.48-times at 14 days of mulch degradation compared with that before degradation, and Acidophilus phylum (14 days) decreased by 99.33%. The abundance of fungal communities was elevated in relation to the main functional microorganisms involved in liquid mulch degradation, with Alternaria and Cladosporium of the Ascomycete phylum Zygomycetes being the most active at the early stage of mulch degradation (7 days), and the relative abundance of Blastocystis was significantly elevated at the late stage of mulch degradation (14 days), which increased by 13.32%. This study provides important support for the green and sustainable development of modern agriculture.

Effects of Different Forms of Tagetes erecta Biofumigation on the Growth of Apple Seedlings and Replanted Soil Microbial Environment

Apple replant disease (ARD) is a common soil disease that occurs in apple-growing areas around the world, causing root tip rot and necrosis, plant growth retardation and even plant death. Biofumigation is a promising strategy for controlling ARD due to its advantages of convenient application and being environmentally friendly. Tagetes erecta is an effective biological fumigant, but its effect on ARD is unclear. In the present study, we used Malus hupehensis Rehd. seedlings as the test material to detect the mitigating effects of different forms of T. erecta: air-dried sample (DS), fresh samples (FS) and fresh sample infusion solution (IS) on ARD. The effects of different forms of T. erecta on the growth of apple seedlings, leaf photosynthesis, root antioxidant enzyme, soil enzymatic activity and microbial environment were investigated. Compared with the CK treatments, DS, FS, and IS treatments all significantly increased the biomass of apple seedlings and promoted root growth under replanting conditions. Among them, DS showed the best results. The activity of antioxidant enzyme including superoxide dismutase, peroxidase and catalase were significantly increased in roots grown in soils treated with T. erecta. Moreover, T. erecta treatment also increased the activity of soil urease, phosphatase, sucrase and catalase enzyme, significantly altered the abundance of soil fungal communities and, in particular, reduced the abundance of Fusarium oxysporum, the main causal fungus of ARD. Therefore, our results suggest that biofumigation of different forms of T. erecta enhanced the resistance of ARD by regulating root reactive oxygen levels and improving the soil fungal communities.

Characteristics of Soil Fungal Communities in Soybean Rotations

Soybean continuous cropping (SC) leads to continuous cropping obstacles, and soil-borne fungal diseases occur frequently. Rotation can alleviate continuous cropping obstacles. However, the long-term effects of continuous cropping and rotation on the structure and function of the fungal community in soil are not clear. In this study, five cropping systems, SC, fallow (CK), fallow-soybean (FS), corn–soybean (CS), and wheat–soybean (WS), were implemented in the long-term continuous cropping area of soybean. After 13 years of planting, high-throughput sequencing was used to evaluate the structure and diversity of soil fungal communities and to study the relationship between fungal communities and soil environmental factors. The results showed that the abundance and diversity of fungal flora in SC soil were the highest. There were significant differences in the formation of soil fungal communities between soybean continuous cropping and the other treatments. There were 355 species of endemic fungi in SC soil. There were 231 and 120 endemic species in WS and CS, respectively. The relative abundance of the potential pathogens Lectera, Gibberella, and Fusarium in the SC treatment soil was significantly high, and the abundance of all potential pathogens in CK was significantly the lowest. The abundance of Lectera and Fusarium in CS was significantly the lowest. There was a positive correlation between potential pathogens in the soil. The relative abundance of potential pathogens in the soil was significantly positively correlated with the relative abundance of Ascomycetes and negatively correlated with the relative abundance of Basidiomycetes. Potential pathogenic genera had a significant negative correlation with soil OM, available Mn, K and soil pH and a significant positive correlation with the contents of soil available Cu, Fe, and Zn. In general, the fungal communities of SC, FS, WS, and CS were divided into one group, which was significantly different from CK. WS and CS were more similar in fungal community structure. The CK and CS treatments reduced the relative abundance of soil fungi and potential pathogens. Our study shows that SC and FS lead to selective stress on fungi and pathogenic fungi and lead to the development of fungal community abundance and diversity, while CK and CS can reduce this development, which is conducive to plant health.

Response of Soil Fungal Communities in Diversified Rotations of Wheat and Different Crops

Crop-soil microorganism interactions and feedback are critical to soil health and crop production. The aim of this study was to clarify the difference in soil fungal communities under diversified rotations of wheat and different crops in the North China Plain and to provide a theoretical basis for the construction and optimization of ecological sustainable planting systems. The soil fungal community abundance, composition, and diversity of continuous winter wheat-summer maize M, winter wheat-summer peanut (summer maize) PM, and winter wheat-summer soybean (summer maize) SM treatments were studied using real-time quantitative PCR and high-throughput sequencing technology. The results showed that, compared with those of the continuous winter wheat-summer maize treatment, the peanut rotation treatment PM2 and soybean rotation treatment SM2 significantly reduced soil fungal ITS sequence copy numbers (P<0.05); there was no significant difference in soil fungal ITS sequence copy numbers between other rotation treatments and those of the control (P>0.05). Rotation treatments with peanut or soybean increased soil fungal community richness (Chao1 and ACE indices) and diversity (Shannon and InvSimson indices), in which the community richness of all rotation treatments and the community diversity of SM1/SM2 treatments varied significantly (P<0.05). The result of non-metric multidimensional scaling (NMDS) analysis showed that the soil fungal community among different rotation crops were obviously separated. The rotation crops significantly affected soil fungal community structure (PERMANOVA:r2=0.350, P=0.001; ANOSIM:r=0.478, P=0.001). Ascomycota (73.67%-85.48%) was the dominant phylum, whereas Sordariomycetes (30.53%-48.19%) and Eurotiomycetes (11.12%-31.19%) were the dominant classes of the fungal communities of sandy-loam fluvo-aquic soil in the North China Plain. There were significantly different taxa of soil fungal communities in different rotations. Potential pathogens such as Neocosmospora, Plectosphaerella, and Gibellulopsis were significantly enriched in the rotations of winter wheat-summer peanut (summer maize), whereas potential beneficial fungi such as Penicillium and Zopfiella were significantly enriched in the rotations of winter wheat-summer soybean (summer maize). Compared with that under the continuous winter wheat-summer maize treatment, rotations with peanut or soybean increased the relative abundance of pathotroph, pathotroph-symbiotroph, and saprotroph-symbiotroph fungi and decreased the relative abundance of saprotroph fungi. The soil fungal community richness and structure were significantly related to soil organic carbon and available nutrients, and the Shannon diversity index was significantly related to soil mineral nitrogen and available phosphorus. In summary, on the basis of continuous winter wheat-summer maize rotation in the North China Plain, adding summer peanut or summer soybean instead of summer maize for rotations with different interval years could increase the richness and diversity of soil fungal communities and significantly change soil fungal community structure. In particular, summer soybean as the preceding crop had a positive effect on the enrichment of potential beneficial fungi.

Assessing the Effect of Physicochemical Properties of Saline and Sodic Soil on Soil Microbial Communities

Soil physicochemical properties are the main driving factors affecting the stability and diversity of the soil microbial community. The impacts of the saline–alkali situation and associated soil degradation need to be understood and reversed as soil diversity and communities are increasingly affected by saline–alkaline soil. However, the differences between salinization and alkalization soil and their impact on microbiota have been overlooked. The object of this study is to demonstrate the differences in salinization and alkalization soil and the driving factors affecting microbiota. In this study, 12 soil samples collected from saline–alkaline spots were used to detect the differences in soil physicochemical properties. The soil microbial community was sequenced by high-throughput sequencing. The results of ESP and EC in the soil samples indicated that the soil samples were categorized as saline soil and sodic soil. Venn diagrams indicated that unique OTUs in saline soil showed higher adaptation and environmental tolerance. Partial Mantel tests showed that the differences in pH, exchangeable sodium percentage (ESP), C/N, Na, and K between saline and sodic soil were the primary determinants affecting the relative abundance of bacterial and fungal communities, besides electrical conductivity (EC). In the KEGG analysis, ESP mainly affected the cellular processes in the archaea. Metabolism in the bacterial function was positively correlated with K only in sodic soil. These results indicated that the proportions in sodic soil were more strongly affecting soil microbiota.

Physicochemical Variables Better Explain Changes in Microbial Community Structure and Abundance under Alternate Wetting and Drying Events

Soil microbial communities play an important role in nutrient cycling; however, their response under repeated long-term fertilization has attracted little attention and needs further appraisal. A 14-day incubation study compared the relative abundance, diversity, and composition of bacterial and fungal microbial communities in soils treated with long-term applications of chemical fertilizer (CF), pig manure plus chemical fertilizer (PMCF), and rice straw plus chemical fertilizer (SRCF) in a paddy field. A high-throughput sequencing approach was applied to assess the diversity and composition of microbial community. Results revealed the Shannon index of the bacterial community decreased with fertilizer addition but increased in case of fungal community. The abundance of the Actinobacteria was higher in the PMCF, while Proteobacteria were higher in the CF and SRCF treatments than those in the unamended control under alternate wetting and drying (AWD) and permanent flooding (PF). In addition, chemical fertilizer history increased the abundance of Firmicutes under AWD. Initially, Nitrospira were found higher in the unamended control than in the amended treatments, but an increase was observed with time in fertilized treatments. Among all genera, Proteobacteria were the most abundant bacterial genus. The main properties that markedly affected the bacterial communities were SOC (R2 = 0.4037, p &lt; 0.02), available P (R2 = 0.3273, p &lt; 0.05), and NO3− (R2 = 0.3096, p &lt; 0.08). Soil physicochemical factors and biogenic factors explained a variation of 46.27% and 29.35%, respectively. At the same time, 4.59% was the combined effect of physicochemical and biogenic factors. Our results suggested that the physicochemical properties had a more significant impact on bacterial activities than water regime by increasing N and organic matter concentrations in the soils.

Microbial community day-to-day dynamics during a spring algal bloom event in a tributary of Three Gorges Reservoir

The microbial food-loop is critical to energy flow in aquatic food webs. We tested the hypothesis that species composition and relative abundance in a microbial community would be modified by the development of toxic algal blooms either by enhanced carbon production or toxicity. This study tracked the response of the microbial community with respect to composition and relative abundance during a 7-day algal bloom event in the Three Gorges Reservoir in May 2018. Chlorophyll a biomass, microscopic identification and cell counting of algae and algal abundance (ind. L−1) and carbon, nutrient concentrations (total phosphorus and nitrogen, dissolved total phosphorus and nitrogen), and DNA high throughput sequencing were measured daily. Algal density (1.2 × 109 ind. L−1) and Chlorophyll a (219 μg L−1) peaked on May 20th–21st, when the phytoplankton community was dominated by Chlorella spp. and Microcystis spp. The concentrations of both dissolved total nitrogen and phosphorus declined during the bloom period. Based on DNA high throughput sequencing data, the relative abundance of eukaryotic phytoplankton, microzooplankton (20–200 μm), mesozooplankton (>200 μm), and fungal communities varied day by day while the prokaryotic community revealed a more consistent structure. Enhanced carbon production during the bloom was closely associated with increased heterotrophic microbial composition in both the prokaryotic and eukaryotic communities. A storm event, however, that caused surface cooling and deep mixing of the water column greatly modified the composition and relative abundance of species in the microbial loop. The high temporal variability and dynamics observed in this study suggest that many factors, and not just algal blooms, were interacting to determine the composition and relative abundance of species of the microbial loop.

Litter Mixing Alters Microbial Decomposer Community to Accelerate Tomato Root Litter Decomposition.

ABSTRACTMixing plant litters of multiple species can alter litter decomposition, a key driver of carbon and nutrient cycling in terrestrial ecosystems. Changes in microbial decomposer communities is proposed as one of the mechanisms explaining this litter-mixture effect, but the underlying mechanism is unclear. In a microcosm litterbag experiment, we found that, at the early stage of decomposition, litter mixing promoted tomato root litter decomposition, thus generating a synergistic nonadditive litter-mixture effect. The transplanting decomposer community experiment showed that changes in microbial decomposer communities contributed to the nonadditive litter-mixture effect on tomato root litter decomposition. Moreover, litter mixing altered the abundance and diversity of bacterial and fungal communities on tomato root litter. Litter mixing also stimulated several putative keystone operational taxonomic units (OTUs) in the microbial correlation network, such as Fusarium sp. fOTU761 and Microbacterium sp. bOTU6632. Then, we isolated and cultured representative isolates of these two taxa, named Fusarium sp. F13 and Microbacterium sp. B26. Subsequent in vitro tests found that F13, but not B26, had strong decomposing ability; moreover, these two isolates developed synergistic interaction, thus promoted litter decomposition in coculture. Addition of F13 or B26 both promoted the decomposing activity of the resident decomposer community on tomato root litter, confirming their importance for litter decomposition. Overall, litter mixing promoted tomato root litter decomposition through altering microbial decomposers, especially through stimulating certain putative keystone taxa.IMPORTANCE Microbial decomposer community plays a key role in litter decomposition, which is an important regulator of soil carbon and nutrient cycling. Though changes in decomposer communities has been proposed as one of the potential underlying mechanisms driving the litter-mixture effects, direct evidence is still lacking. Here, we demonstrated that litter mixing stimulated litter decomposition through altering microbial decomposers at the early stage of decomposition. Moreover, certain putative keystone taxa stimulated by litter mixing contributed to the nonadditive litter-mixture effect. In vitro culturing validated the role of these taxa in litter decomposition. This study also highlights the possibility of regulating litter decomposition through manipulating certain microbial taxa.

Minimizing tillage modifies fungal denitrifier communities, increases denitrification rates and enhances the genetic potential for fungal, relative to bacterial, denitrification

Nitrous oxide (N2O) emissions from arable soils are predominantly caused by denitrifying microbes, of which fungal denitrifiers are of particular interest, as fungi, in contrast to bacteria, terminate denitrification with N2O. Reduced tillage has been shown to increase gaseous nitrogen losses from soil, but knowledge of how varying tillage regimes and associated soil physical and chemical alterations affect fungal denitrifiers is limited. Based on results from a long-term (>40 years) tillage experiment, we show that non-inversion tillage resulted in increased potential denitrification activity in the upper soil layers, compared to annual or occasional (every 4–5 years) conventional inversion tillage. Using sequence-corrected abundance of the fungal nirK gene, we further identified an increased genetic potential for fungal denitrification, compared to that caused by bacteria, with decreasing tillage intensity. Differences in the composition and diversity of the fungal nirK community imply that different tillage regimes select for distinct fungal denitrifiers with differing functional capabilities and lifestyles, predominantly by altering carbon and nitrogen related niches. Our findings suggest that the creation of organic hotspots through stratification by non-inversion tillage increases the diversity and abundance of fungal denitrifier communities and modifies their composition, and thus their overall relevance for N2O production by denitrification, in arable soils.

HPLC and high-throughput sequencing revealed higher tea-leaves quality, soil fertility and microbial community diversity in ancient tea plantations: compared with modern tea plantations

BackgroundAncient tea plantations with an age over 100 years still reserved at Mengku Town in Lincang Region of Yunan Province, China. However, the characteristic of soil chemicophysical properties and microbial ecosystem in the ancient tea plantations and their correlation with tea-leaves chemical components remained unclear. Tea-leaves chemical components including free amino acids, phenolic compounds and purine alkaloids collected from modern and ancient tea plantations in five geographic sites (i.e. Bingdao, Baqishan, Banuo, Dongguo and Jiulong) were determined by high performance liquid chromatography (HPLC), while their soil microbial community structure was analyzed by high-throughput sequencing, respectively. Additionally, soil microbial quantity and chemicophysical properties including pH, cation exchange capacity (CEC), soil organic matter (SOM), soil organic carbon (SOC), total nitrogen (TN), total phosphorus (TP), total potassium (TK), alkali-hydrolyzable nitrogen (AN), available phosphorous (AP) and available potassium (AK) were determined in modern and ancient tea plantations.ResultsTea-leaves chemical components, soil chemicophysical properties and microbial community structures including bacterial and fungal community abundance and diversity evaluated by Chao 1 and Shannon varied with geographic location and tea plantation type. Ancient tea plantations were observed to possess significantly (P < 0.05) higher free amino acids, gallic acid, caffeine and epigallocatechin (EGC) in tea-leaves, as well as soil fertility. The bacterial community structure kept stable, while fungal community abundance and diversity significantly (P < 0.05) increased in ancient tea plantation because of higher soil fertility and lower pH. The long-term plantation in natural cultivation way might significantly (P < 0.05) improve the abundances of Nitrospirota, Methylomirabilota, Ascomycota and Mortierellomycota phyla.ConclusionsDue to the natural cultivation way, the ancient tea plantations still maintained relatively higher soil fertility and soil microbial ecosystem, which contributed to the sustainable development of tea-leaves with higher quality.

Pine species determine fungal microbiome composition in a common garden experiment

The factors shaping the composition of microbial communities in trees remain poorly understood. We evaluated whether the core and satellite fungal communities in five pine species ( Pinus radiata, Pinus pinaster, Pinus sylvestris, Pinus nigra, and Pinus uncinata ) were shaped by the host species identity. Because the trees had earlier been inoculated with a fungal pathogen ( Fusarium circinatum ), we also explored the possibilities to detect its presence and potential co-occurrence networks. We found interspecific variation in the fungal community composition and abundance among the different tree species and the existence of a core microbiome that was independent of the host species. The presence of F. circinatum was confirmed in some samples through qPCR but the pathogen did not co-occur with a specific fungal community. The results highlight the importance of host species as a determinant of microbiome assembly in common environments.

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.

Linking carbon-degrading enzyme activity to microbial carbon-use trophic strategy under salinization in a subtropical tidal wetland

Although increasing studies have reported that microorganisms play an important role in carbon (C)-degrading enzyme activities under salinization, there is little experimental evidence for the associations between C-degrading enzyme activities and microbial community structure. Here, we examined the C-degrading enzyme activities, bacterial and fungal community abundance and composition (16S and ITS rRNA gene sequencing), soil organic carbon (SOC) storage, carbon/nitrogen (C/N) ratios, labile organic carbon (LOC) levels, and LOC/SOC ratios along an estuarine salinity gradient [range: 0.1–2.2 part per thousand (ppt)] of a subtropical tidal wetland. To help isolate salinity effects, sampling sites were selected to be similar in plant community composition, soil texture, and tidal influence. Our results indicated that the SOC storage, LOC levels, and LOC/SOC ratios decreased, whereas C/N ratios increased with salinization. The activities of β-1,4-glucosidase, cellobiohydrolase, phenol oxidase, and peroxidase increased by 485%, 147%, 699%, and 868%, respectively, with increasing salinity. The α-diversities of bacterial and fungal communities did not change, whereas the abundances of bacterial and fungal communities decreased with increasing salinity. Both bacterial and fungal oligotrophs/copiotrophs ratios were positively associated with salinity, suggesting that bacterial and fungal communities shifted from being copiotroph-dominated to oligotroph-dominated as salinity increased. All C-degrading enzyme activities were correlated with the relative abundance of typical bacterial and fungal oligotrophs, e.g., α-Proteobacteria, δ-Proteobacteria, Chloroflexi, Acidobacteria, and Basidiomycota. Overall, the C-degrading enzyme activities were co-determined by the C/N and LOC/SOC ratios and the fungal and bacterial oligotrophs/copiotrophs ratios. Our observations indicated that salinization influenced C-degrading enzyme activities via modulating substrate quality and lability and causing shifts in microbial C-use trophic strategies. Our proposed oligotrophic–copiotrophic scheme could be a novel method for incorporating vast taxonomic data of microbial communities into enzyme activity prediction in an ecologically meaningful manner.