Mycorrhizal effects on crop yield and soil ecosystem functions in a long-term tillage and fertilization experiment.

It is well understood that agricultural management influences arbuscular mycorrhizal (AM) fungi, but there is controversy about whether farmers should manage for AM symbiosis. We assessed AM fungal communities colonizing wheat roots for three consecutive years in a long-term (> 14 yr) tillage and fertilization experiment. Relationships among mycorrhizas, crop performance, and soil ecosystem functions were quantified. Tillage, fertilizers and continuous monoculture all reduced AM fungal richness and shifted community composition toward dominance of a few ruderal taxa. Rhizophagus and Dominikia were depressed by tillage and/or fertilization, and their abundances as well as AM fungal richness correlated positively with soil aggregate stability and nutrient cycling functions across all or no-tilled samples. In the field, wheat yield was unrelated to AM fungal abundance and correlated negatively with AM fungal richness. In a complementary glasshouse study, wheat biomass was enhanced by soil inoculum from unfertilized, no-till plots while neutral to depressed growth was observed in wheat inoculated with soils from fertilized and conventionally tilled plots. This study demonstrates contrasting impacts of low-input and conventional agricultural practices on AM symbiosis and highlights the importance of considering both crop yield and soil ecosystem functions when managing mycorrhizas for more sustainable agroecosystems.

Dominance by cyanobacteria in the newly formed biofilms on stone monuments under a protective shade at the Beishiku Temple in China.

Following the installation of a protective shade, rapid propagation of microorganisms showing in black and grey colors occurred at Beishiku Temple in Gansu Province of China. This study employed a combination of high-throughput sequencing technology, morphological examinations, and an assessment of the surrounding environmental condition to analyze newly formed microbial disease spots. The investigation unveiled the responsible microorganisms and the instigating factors of the microbial outbreak that subsequently to the erection of the shade. Through comparison of bioinformatics, the ASV method surpasses the OTU method in characterizing community compositional changes by the dominant microbial groups, the phylum Cyanobacteria emerged as the most dominant ones in the microbial community accountable for the post-shade microbial deterioration. The black spot and grey spot are predominantly composed of Mastigocladopsis and Scytonema, respectively. Validation analysis, based on the active RNA-level community results, supported and validated these conclusions. Comparative scrutiny of the microbial community before shade installation and the background environmental data disclosed that the erection of the shade prompted a decrease in temperatures and an increase in humidity within the protected area. Consequently, this spurred the exponential proliferation of indigenous cyanobacteria in the spots observed. The outcomes of this study carry considerable significance in devising preventive conservation strategies for cultural heritage and in managing the process of biodeterioration.

Slope aspect determines the abundance and composition of nitrogen-cycling microbial communities in an alpine ecosystem.

Slope aspect is an important topographic feature that can influence local environmental conditions. While strong effects of slope aspect on aboveground and belowground communities have been frequently elucidated, how slope aspect affects soil nitrogen (N) cycling microbes remains unclear. Here, we characterized the communities of soil N-cycling microbes on south- and north-facing slopes in an alpine ecosystem, by quantifying (qPCR) and high-throughput sequencing six genes involved in N-fixation (nifH), nitrification (archaeal and bacterial amoA) and denitrification (nirK, nirS and nosZ). We found that the abundance, diversity and community composition of major N-cycling microbes differed dramatically between the two slope aspects, and these variances could be well explained by the aspect-driven differences in environmental conditions, especially soil temperature and moisture. The response patterns of different N-cycling groups to slope aspect were much inconsistent, especially for those with similar functions (i.e. ammonia-oxidizing archaea vs. bacteria, nirK- vs. nirS-reducers), indicating strong niche differentiation between these counterparts. We also observed strong preferences and distinct co-occurrence patterns of N-cycling microbial taxa for the two slope aspects. These findings highlight the importance of slope aspect in determining the abundance, species distribution and community structure of N-cycling microbes, and consequently influencing N-cycling processes and ecosystem functioning.

The presence of Toxoplasma gondii in soil, their transmission, and their influence on the small ruminants and human population: A review.

The ecosystem approach has been developed since the 1940s. An ecosystem is a community of living organism and their interaction and conjugation with abiotic factors of the environment. The ecosystem is not endemic to the aquatic environment only but, the terrestrial environment is also considered to be a part of an ecosystem. Soil act as mother role for the survival of different microorganism. The Toxoplasma gondii oocysts stay survive for a long time in the soil. This presence of these oocysts might critically enhance the success of this parasite in two ways. First, this parasite can widespread; second, it can create a lot of consequences regarding animals and their economic value. Soil contamination caused by Toxoplasma gondii Y is a significant and profound issue for animals and public health. Therefore, the current study was aimed to summarize and correlate the soil and parasite, their transmission, infection, and some aspects related to T. gondii. The small animals are pose at a high risk therefore, it was concluded that some preventive measures should be taken to keep secure itself from zoonotic diseases.

Arbuscular mycorrhizal fungi serve as keystone taxa for revegetation on the Tibetan Plateau.

Revegetation is widely used to enhance degraded topsoil recovery with the enhancements of soil nutrient accumulation and soil structure stabilization. Arbuscular mycorrhizal fungi (AMF) are important for the allocation of carbon into the soil and the formation of soil aggregates. Thus, we hypothesized that AMF could construct more niches for other microbes during revegetation, making AMF keystone taxa of soil. Soil fungal and bacterial communities were investigated under a revegetation experiment and correlation networks between soil fungi and bacteria were constructed. Simultaneously, the plant growth level, soil properties and structure, and soil microbial carbon decomposition abilities were measured. The results revealed that AMF were the most central fungi at the phylum (degree = 3), class (degree = 11), and family (degree = 15) levels. The reads number of AMF were positively correlated with both fungal (R2 = 0.431, P < 0.001) and bacterial (R2 = 0.106, P = 0.044) richness. Higher colonization of AMF in roots and/or more AMF extraradical mycelium and spores in soil indicated a better plant growth, more stable soil aggregates, and a higher carbon decomposition ratio. Our results highlight that AMF are keystone taxa in revegetation, as they play significant roles in enhancing the recovery of the belowground microbiome diversity, soil structure stability, and nutrients cycling. The positive roles of AMF in revegetation support the application of AMF in ecosystem recovery.

Revegetation differentially influences microbial trophic groups in a Qinghai-Tibetan alpine steppe ecosystem.

Revegetation accelerates the recovery of degraded lands. Different microbial trophic groups underpin this acceleration from the aspects of soil structure stabilization, nutrient accumulation, and ecosystem functions. However, little is known about how revegetation influences the community and biodiversity of different soil microbial trophic groups. Here, six revegetation treatments with different plantings of plant species were established at an excavation pit in the Qinghai-Tibetan Plateau. Communities of plant, bacteria, and several key soil fungal groups were investigated after 12 years of revegetation. Plant and all microbial trophic group compositions were markedly influenced by revegetation treatments. Total fungal and pathogenic fungal compositions were not significantly predicted by any factor of plant and soil, but arbuscular mycorrhizal fungal composition could be mainly predicted by plant composition and plant P content. Bacterial composition was mainly determined by soil total N, organic carbon concentration, and moisture content; and saprotrophic fungal composition was mainly determined by soil organic carbon. Soil pH was the strongest factor to predict bacterial metabolic functions. Our findings highlight that even the differences of microbial compositions were because of different revegetation treatments, but each trophic microbial composition had different relations with plant and/or soil; especially, the bacterial community and metabolic functions and saprotrophic fungal community were more correlated with soil properties rather than plant community or characteristics per se.

Mechanistic Insights into Arbuscular Mycorrhizal Fungi-Mediated Drought Stress Tolerance in Plants.

Arbuscular mycorrhizal fungi (AMF) establish symbiotic interaction with 80% of known land plants. It has a pronounced impact on plant growth, water absorption, mineral nutrition, and protection from abiotic stresses. Plants are very dynamic systems having great adaptability under continuously changing drying conditions. In this regard, the function of AMF as a biological tool for improving plant drought stress tolerance and phenotypic plasticity, in terms of establishing mutualistic associations, seems an innovative approach towards sustainable agriculture. However, a better understanding of these complex interconnected signaling pathways and AMF-mediated mechanisms that regulate the drought tolerance in plants will enhance its potential application as an innovative approach in environmentally friendly agriculture. This paper reviews the underlying mechanisms that are confidently linked with plant-AMF interaction in alleviating drought stress, constructing emphasis on phytohormones and signaling molecules and their interaction with biochemical, and physiological processes to maintain the homeostasis of nutrient and water cycling and plant growth performance. Likewise, the paper will analyze how the AMF symbiosis helps the plant to overcome the deleterious effects of stress is also evaluated. Finally, we review how interactions between various signaling mechanisms governed by AMF symbiosis modulate different physiological responses to improve drought tolerance. Understanding the AMF-mediated mechanisms that are important for regulating the establishment of the mycorrhizal association and the plant protective responses towards unfavorable conditions will open new approaches to exploit AMF as a bioprotective tool against drought.

Dynamics of arbuscular mycorrhizal fungal community structure and functioning along a nitrogen enrichment gradient in an alpine meadow ecosystem.

Nitrogen (N) availability is increasing dramatically in many ecosystems, but the influence of elevated N on the functioning of arbuscular mycorrhizal (AM) fungi in natural ecosystems is not well understood. We measured AM fungal community structure and mycorrhizal function simultaneously across an experimental N addition gradient in an alpine meadow that is limited by N but not by phosphorus (P). AM fungal communities at both whole-plant-community (mixed roots) and single-plant-species (Elymus nutans roots) scales were described using pyro-sequencing, and the mycorrhizal functioning was quantified using a mycorrhizal-suppression treatment in the field (whole-plant-community scale) and a glasshouse inoculation experiment (single-plant-species scale). Nitrogen enrichment progressively reduced AM fungal abundance, changed AM fungal community composition, and shifted mycorrhizal functioning towards parasitism at both whole-plant-community and E. nutans scales. N-induced shifts in AM fungal community composition were tightly linked to soil N availability and/or plant species richness, whereas the shifts in mycorrhizal function were associated with the communities of specific AM fungal lineages. The observed changes in both AM fungal community structure and functioning across an N enrichment gradient highlight that N enrichment of ecosystems that are not P-limited can induce parasitic mycorrhizal functioning and influence plant community structure and ecosystem sustainability.

Anthropogenic disturbance equalizes diversity levels in arbuscular mycorrhizal fungal communities.

The arbuscular mycorrhizal (AM) symbiosis is a key plant-microbe interaction in sustainable functioning ecosystems. Increasing anthropogenic disturbance poses a threat to AM fungal communities worldwide, but there is little empirical evidence about its potential negative consequences. In this global study, we sequenced AM fungal DNA in soil samples collected from pairs of natural (undisturbed) and anthropogenic (disturbed) plots in two ecosystem types (10 naturally wooded and six naturally unwooded ecosystems). We found that ecosystem type had stronger directional effects than anthropogenic disturbance on AM fungal alpha and beta diversity. However, disturbance increased alpha and beta diversity at sites where natural diversity was low and decreased diversity at sites where natural diversity was high. Cultured AM fungal taxa were more prevalent in anthropogenic than natural plots, probably due to their efficient colonization strategies and ability to recover from disturbance. We conclude that anthropogenic disturbance does not have a consistent directional effect on AM fungal diversity; rather, disturbance equalizes levels of diversity at large scales and causes changes in community functional structure.

Description of Naumannella cuiyingiana sp. nov., isolated from a ca. 1500-year-old mural painting, and emended description of the genus Naumannella.

Strain AFT2T was isolated from a mural painting sample from a ca. 1500-year-old tomb located in Shanxi Province, China. The isolate was a Gram-stain-positive, non-motile, non-spore-forming, aerobic and oval to short-rod-shaped bacterium that formed white-pigmented colonies. Phylogenetic analyses based on 16S rRNA gene sequence revealed that strain AFT2T was most closely (97.01 %) correlated and formed a monophyletic clade with Naumannella halotolerans WS4616T (=DSM 24323T). The G+C content of the genomic DNA was 71.97 mol%, and the strain showed 37.27 % DNA-DNA relatedness to N. halotolerans DSM 24323T. The major cellular fatty acid was anteiso-C15 : 0 (55.32 %), and MK-9(H4) was the only respiratory quinone. The polar lipids comprised phosphatidylglycerol, diphosphatidylglycerol, two unknown phospholipids and five unknown glycolipids. ll-Diaminopimelic acid was detected in the cell-wall peptidoglycan (type A3γ), and the whole-cell sugars consisted of ribose, mannose, arabinose and galactose. On the basis of its phenotypic and phylogenetic characteristics, it is proposed that strain AFT2T should be classified as a representative of a novel species of the genus Naumannella, for which the name Naumannella cuiyingiana sp. nov. is proposed. The type strain is AFT2T (=CCTCC AB 2015428T=DSM 103164T).

Characterization of the prokaryotic diversity through a stratigraphic permafrost core profile from the Qinghai-Tibet Plateau.

Permafrost on the Qinghai-Tibet Plateau is one of the most sensitive regions to climate warming, thus characterizing its microbial diversity and community composition may be important for understanding their potential responses to climate changes. Here, we investigated the prokaryotic diversity in a 10-m-long permafrost core from the Qinghai-Tibet Plateau by restriction fragment length polymorphism analysis targeting the 16S rRNA gene. We detected 191 and 17 bacterial and archaeal phylotypes representing 14 and 2 distinct phyla, respectively. Proteobacteria was the dominant bacterial phylum, while archaeal communities were characterized by a preponderance of Thaumarchaeota. Some of prokaryotic phylotypes were closely related to characterized species involved in carbon and nitrogen cycles, including nitrogen fixation, methane oxidation and nitrification. However, the majority of the phylotypes were only distantly related to known taxa at order or species level, suggesting the potential of novel diversity. Additionally, both bacterial α diversity and community composition changed significantly with sampling depth, where these communities mainly distributed according to core horizons. Arthrobacter-related phylotypes presented at high relative abundance in two active layer soils, while the deeper permafrost soils were dominated by Psychrobacter-related clones. Changes in bacterial community composition were correlated with most measured soil variables, such as carbon and nitrogen contents, pH, and conductivity.

The microbial diversity, distribution, and ecology of permafrost in China: a review.

Permafrost in China mainly located in high-altitude areas. It represents a unique and suitable ecological niche that can be colonized by abundant microbes. Permafrost microbial community varies across geographically separated locations in China, and some lineages are novel and possible endemic. Besides, Chinese permafrost is a reservoir of functional microbial groups involved in key biogeochemical cycling processes. In future, more work is necessary to determine if these phylogenetic groups detected by DNA-based methods are part of the viable microbial community, and their functional roles and how they potentially respond to climate change. This review summaries recent studies describing microbial biodiversity found in permafrost and associated environments in China, and provides a framework for better understanding the microbial ecology of permafrost.

Comparison of different PCR primers on detecting arbuscular mycorrhizal communities inside plant roots.

OBJECTIVE: Communities of arbuscular mycorrhizal fungi (AMF) colonizing roots have been increasingly investigated by molecular approaches with AMF-specific PCR primers. However, it is difficult to compare the species diversity and species compositions of AMF communities across various studies due to the PCR primers used differently, and also little is known if significant difference of community compositions is characterized by different primers. We aim to compare the difference of efficiency of four primers for AMF. METHODS: We chose four commonly used AMF-specific primer combinations (NS31-AM1, AMLl-AML2, NS31-AML2 and SSUmCf-LSUmBr), and used 18S rDNA clone libraries to describe the AMF diversity and community. RESULTS: Our results showed that the specificity and coverage varied among the tested primers, different primer combinations would yield distinct patterns of species diversity and composition of AMF community. SSUmCf-LSUmBr had the best specificity and coverage in amplifying AMF sequences, followed by NS31-AML2 and NS31-AM1, and AML1-AML2 showed the lowest specificity towards AMF sequences. CONCLUSION: SSUmCf-LSUmBr is not the optimal primer pair for AMF community study in current stage due to limited reference sequences and large DNA size. As an alternative, NS31-AML2 is more suitable in AMF community study, because its target rDNA region could well match the increasingly used virtual taxonomy database (http://maarjam. botany.ut.ee) and also its suitable DNA size could be efficiently used in high-throughput sequencing.

Microcalorimetric study of the effects of long-term fertilization on soil microbial activity in a wheat field on the Loess Plateau.

The effects of the long-term inorganic (nitrogen, N; phosphate, P) and organic (manure, M; straw, S) fertilizers/managemenet individually and in combinations (N, NP, SNP, M, and MNP) on soil microbial activity were investigated in a wheat field on the Loess Plateau, China. Microcalorimetry was used to determine microbial activity under different treatments. Nearly 30 years of consecutive fertilization has altered the culturable population of soil bacteria and fungi, the highest ones were detected in the treatments of manure and MNP, followed by the NP and SNP treatments. The microbial growth rate constant (µ/h(-1)) was significantly greater in the MNP treatment than all the other treatments. The total heat exchange values (Q/J) were the highest in the MNP and NP treatments, which were significantly different from the N and M treatments. The peak height (P(t)/µW) were significantly higher in MNP and NP treatments than in the remaining treatments. The peak time values (t(p)/h) among the MNP, NP, SNP and M, N and CK treatments were significantly different. In general, comparing with control, soil microbial activity was much higher in MNP, NP and SNP treatments, all including the phosphate fertilizer. Our results showed that the application of inorganic fertilizer and organic manure have positive effects on multiple soil chemical parameters, soil microorganism abundance and activity, and hence crop yield.

Effects of enhanced UV-B radiation on the diversity and activity of soil microorganism of alpine meadow ecosystem in Qinghai-Tibet Plateau.

The effects of enhanced UV-B radiation on abundance, community composition and the total microbial activity of soil bacteria in alpine meadow ecosystem of Qinghai-Tibet Plateau were investigated. Traditional counting and 16S rRNA gene sequencing were used to investigate the culturable bacteria and their composition in soil, meanwhile the total microbial activity was measured by microcalorimetry. The population of soil culturable bacteria was slightly reduced with the enhanced UV-B radiation in both of the two depths, 2.46 × 10(6) CFU/g in upper layer (0-10 cm), 1.44 × 10(6) CFU/g in under layer (10-20 cm), comparing with the control (2.94 × 10(6) CFU/g in upper layer, 1.65 × 10(6) CFU/g in under layer), although the difference was not statistically significant (P > 0.05). However, the bacteria diversity decreased obviously due to enhanced UV-B, the number of species for upper layer was decreased from 20 to 13, and from 16 to 13 for the lower layer. The distribution of species was also quite different between the two layers. Another obvious decrease induced by enhanced UV-B radiation was in the total soil microbial activities, which was represented by the microbial growth rate constant (k) in this study. The results indicated that the culturable bacteria community composition and the total activity of soil microbes have been considerably changed by the enhanced UV-B radiation.

Long-term effects of fertilizer on soil enzymatic activity of wheat field soil in Loess Plateau, China.

The effects of long-term (29 years) fertilization on local agro-ecosystems in the Loess Plateau of northwest China, containing a single or combinations of inorganic (Nitrogen, N; Phosphate, P) and organic (Mature, M Straw, S) fertilizer, including N, NP, SNP, M, MNP, and a control. The soil enzymes, including dehydrogenase, urease, alkaline phosphatase, invertase and glomalin, were investigated in three physiological stages (Jointing, Dough, and Maturity) of wheat growth at three depths of the soil profile (0-15, 16-30, 31-45 cm). We found that the application of farmyard manure and straw produced the highest values of soil enzymatic activity, especially a balanced applied treatment of MNP. Enzymatic activity was lowest in the control. Values were generally highest at dough, followed by the jointing and maturity stages, and declined with soil profile depth. The activities of the enzymes investigated here are significantly correlated with each other and are correlated with soil nutrients, in particular with soil organic carbon. Our results suggest that a balanced application of fertilizer nutrients and organic manure (especially those containing P) has positive effects on multiple soil chemical parameters, which in turn enhances enzyme activity. We emphasize the role of organic manure in maintaining soil organic matter and promoting biological activity, as its application can result in a substantial increase in agricultural production and can be sustainable for many years.

Diversity and community structure of fungi through a permafrost core profile from the Qinghai-Tibet Plateau of China.

While a vast number of studies have addressed the prokaryotic diversity in permafrost, characterized by subzero temperatures, low water activity, and extremely low rates of nutrient and metabolite transfer, fungal patterns have received surprisingly limited attention. Here, the fungal diversity and community structure were investigated by culture-dependent technique combined with cloning-restriction fragment length polymorphism (RFLP) analysis of sediments in a 10-m-long permafrost core from the Qinghai-Tibet Plateau of China. A total of 62 fungal phylotypes related to 10 distinct classes representing three phyla were recovered from 5031 clones generated in 13 environmental gene libraries. A large proportion of the phylotypes (25/62) that were distantly related to described fungal species appeared to be novel diversity. Ascomycota was the predominant group of fungi, with respect to both clone and phylotype number. Our results suggested there was the existence of cosmopolitan psychrophilic or psychrotolerant fungi in permafrost sediments, the community composition of fungi varied with increasing depth, while these communities largely distributed according to core layers.

Research progress on ecological adaptation and prevention of Parengyodontium album on the surface of cultural relics.

Cultural relics as the crystallization of human history are non-renewable and irreplaceable resources. Microorganisms are widely colonized on ancient wall paintings, stone cultural relics, and other types of cultural heritages to cause harm. The dominant disease fungus, Parengyodontium album, is extensively distributed and can seriously threaten the long-term preservation of precious cultural heritage due to surviving in various cultural relics and extreme environments. The classification and nomenclature of P. album have undergone several changes, so its impact on cultural relic received little attention. Here, we summarized the brief histories of its classification and development, distribution range, and cultural heritage preference of P. album. We further analyzed the physiological, biochemical, and ecological characteristics and potential biological degradation mechanism. We proposed that P. album could be used as an indicative species of microbial hazardous effects on cultural heritage. We discussed the prevention and control countermeasures of such typical mural microorganisms and pointed out key research directions in this field.

Paracoccus tibetensis sp. nov., isolated from Qinghai-Tibet Plateau permafrost.

Strain Tibet-S9a3(T) was isolated from Qinghai-Tibet Plateau permafrost, China. The isolate was a Gram-negative, non-motile, non-spore-forming short rod. The 16S rRNA gene sequence indicated that strain Tibet-S9a3(T) was a member of the genus Paracoccus and was closely related to Paracoccus aestuarii B7(T) (98.2 % 16S rRNA gene sequence similarity), 'P. beibuensis' JLT1284 (97.9 %), P. homiensis DD-R11(T) (97.4 %), P. zeaxanthinifaciens ATCC 21588(T) (97.4 %) and other type strains of the genus (93.7-96.7 %). The G+C content of the genomic DNA was 69.1 mol% and the major isoprenoid quinone was ubiquinone-10. The major fatty acids were C18 : 1ω7c (87.6 %), C18 : 0 (4.3 %) and C10 : 0 3-OH (2.0 %). DNA-DNA relatedness between strain Tibet-S9a3(T) and P. aestuarii B7(T) was 37.9 %. On the basis of phenotypic and genotypic characteristics, it is suggested that strain Tibet-S9a3(T) represents a novel species of the genus Paracoccus, for which the name Paracoccus tibetensis sp. nov. is proposed. The type strain is Tibet-S9a3(T) ( = CGMCC 1.8925(T)  = NBRC 105667(T)).

Diversity and Composition of Culturable Microorganisms and Their Biodeterioration Potentials in the Sandstone of Beishiku Temple, China.

Microbial colonization on stone monuments leads to subsequent biodeterioration; determining the microbe diversity, compositions, and metabolic capacities is essential for understanding biodeterioration mechanisms and undertaking heritage management. Here, samples of epilithic biofilm and naturally weathered and exfoliated sandstone particles from different locations at the Beishiku Temple were collected to investigate bacterial and fungal community diversity and structure using a culture-based method. The biodeterioration potential of isolated fungal strains was analyzed in terms of pigmentation, calcite dissolution, organic acids, biomineralization ability, and biocide susceptibility. The results showed that the diversities and communities of bacteria and fungi differed for the different sample types from different locations. The population of culturable microorganisms in biofilm samples was more abundant than that present in the samples exposed to natural weathering. The environmental temperature, relative humidity, and pH were closely related to the variation in and distribution of microbial communities. Fungal biodeterioration tests showed that isolated strains four and five were pigment producers and capable of dissolving carbonates, respectively. Their biomineralization through the precipitation of calcium oxalate and calcite carbonate could be potentially applied as a biotechnology for stone heritage consolidation and the mitigation of weathering for monuments. This study adds to our understanding of culturable microbial communities and the bioprotection potential of fungal biomineralization.