Spatio-Temporal Variation of Core and Satellite Arbuscular Mycorrhizal Fungus Communities in Miscanthus giganteus

Year-round dynamics of arbuscular mycorrhizal fungi communities in the roots and surrounding soils of Cryptomeria japonica

Arbuscular mycorrhizal fungi (AMF) live simultaneously inside and outside of host plant roots for a functional mycorrhizal symbiosis. Still, the year-round dynamics and relationships between soil properties and AMF communities of trees in forest ecosystems remain unclear. We collected paired root and soil samples of the same Cryptomeria japonica trees at two forest sites (five trees at each site) every 2 months over a year. Total DNA was extracted from roots and soil separately and soil physicochemical properties were measured. With Illumina's next-generation amplicon sequencing targeting the small subunit of fungal ribosomal DNA, we clarified seasonal dynamics of soil properties and AMF communities. Soil pH and total phosphorus showed significant seasonality while total carbon, nitrogen, and C/N did not. Only pH was a good predictor of the composition and dynamics of the AMF community. The total AMF community (roots + soil) showed significant seasonality because of variation from May to September. Root and soil AMF communities were steady year-round, however, with similar species richness but contained significantly different AMF assemblages in any sampling month. Despite the weak seasonality in the communities, the top two dominant OTUs showed significant but different shifts between roots and soils across seasons with strong antagonistic relationships. In conclusion, few dominant AMF taxa are dynamically shifting between the roots and soils of C. japonica to respond to seasonal and phenological variations in their microhabitats. AMF inhabiting forest ecosystems may have high environmental plasticity to sustain a functional symbiosis regardless of seasonal variations that occur in the soil.

Larger presence of ectomycorrhizae detected from pygmy pine ecotype in the fire-frequent pine barrens ecosystem

Pine barrens ecosystem has acidic, sandy, and nutrient-poor soil and is prone to drought and fire. In the New Jersey Pine Barrens, the predominant pitch pine (Pinus rigida) consists of two ecotypes: the regular pitch pines with heights of 4.6-12 m, and the pygmy pines of low stature (1.2-1.8 m) in the New Jersey Pine Plains. Previous ecological studies suggested that the dwarf pines in the Pine Plains that are embedded within the Pine Barrens were an evolutionary adaptation to frequent fire. Pines are obligate ectomycorrhizal (EcM) mutualists, and their root mycobiota may contribute to stress protection and plant health. However, information on the mycobiota associated with plants in the pine barrens ecosystem is lacking. To have a holistic understanding of the evolution and adaptation in this stressed environment, we used both culture-independent metabarcoding and culture-based method to characterize the mycobiota from soil and root of the two ecotypes and to identify core mycobiota. We found that Agaricomycetes, Leotiomycetes, and Mucoromycotina are predominant fungi in the New Jersey Pine Barrens ecosystem, which is rich in root mutualistic fungi. We observed that the pygmy pine roots had significantly higher density of EcM tips than the regular pine roots. This was corroborated by our metabarcoding analysis, which showed that the pygmy pine trees had higher ratio of ectomycorrhiza-forming fungi than the regular-statured pines. We hypothesize that symbiotrophic EcM fungi associated with pygmy pines are capable of mitigating high fire stress in the Pine Plains.

Arbuscular mycorrhizal fungal communities with contrasting life-history traits influence host nutrient acquisition

Life-history traits differ substantially among arbuscular mycorrhizal (AM) fungal families, potentially affecting hyphal nutrient acquisition efficiency, host nutrition, and thereby plant health and ecosystem function. Despite these implications, AM fungal community life-history strategies and community trait diversity effects on host nutrient acquisition are poorly understood. To address this knowledge gap, we grew sudangrass with AM fungal communities representing contrasting life-history traits and diversity: either (1) five species in the AM family Gigasporaceae, representing competitor traits, (2) five Glomerales species, representing ruderal traits, or (3) a mixed-trait community combining all ten AM fungal species. After 12 weeks, we measured above and belowground plant biomass and aboveground nutrient uptake and concentration. Overall, AM fungal colonization increased host nutrition, biomass, and foliar δ⁵nitrogen enrichment compared to the uncolonized control. Between the single-trait communities, the Glomeraceae community generally outperformed the Gigasporaceae community in host nutrition and plant growth, increasing plant phosphorus (P) uptake 1.5 times more than the Gigasporaceae community. We saw weak evidence for a synergistic effect of the mixed community, which was only higher for plant P concentration (1.26 times higher) and root colonization (1.26 times higher) compared to the single-trait communities. However, this higher P concentration did not translate to more P uptake or the highest plant biomass for the mixed community. These findings demonstrate that the AM symbiosis is affected by community differences at high taxonomic levels and provide insight into how different AM fungal communities and their associated traits affect host nutrition for fast-growing plant species.

Core arbuscular mycorrhizal fungi are predicted by their high abundance-occupancy relationship while host-specific taxa are rare and geographically structured

Habitat restoration may depend on the recovery of plant microbial symbionts such as arbuscular mycorrhizal (AM) fungi, but this requires a better understanding of the rules that govern their community assembly. We examined the interactions of soil and host-associated AM fungal communities between remnant and restored patches of subtropical montane forests. While AM fungal richness did not differ between habitat types, community membership did and was influenced by geography, habitat and host. These differences were largely driven by rare host-specific AM fungi that displayed near-complete turnover between forest types, while core AM fungal taxa were highly abundant and ubiquitous. The bipartite networks in the remnant forest were more specialized and hosts more specific than in the restored forest. Host-associated AM fungal communities nested within soil communities in both habitats, but only significantly so in the restored forest. Our results provide evidence that restored and remnant forests harbour the same core fungal symbionts, while rare host-specific taxa differ, and that geography, host identity and taxonomic resolution strongly affect the observed distribution patterns of these fungi. We suggest that host-specific interactions with AM fungi, as well as spatial processes, should be explicitly considered to effectively re-establish target host and symbiont communities.

Community Assembly and Co-occurrence Patterns Underlying the Core and Satellite Bacterial Sub-communities in the Tibetan Lakes

Microbial communities normally comprise a few core species and large numbers of satellite species. These two sub-communities have different ecological and functional roles in natural environments, but knowledge on the assembly processes and co-occurrence patterns of the core and satellite species in Tibetan lakes is still sparse. Here, we investigated the ecological processes and co-occurrence relationships of the core and satellite bacterial sub-communities in the Tibetan lakes via 454 sequencing of 16S rRNA gene. Our studies indicated that the core and satellite bacterial sub-communities have similar dominant phyla (Proteobacteria, Bacteroidetes, and Actinobacteria). But the core sub-communities were less diverse and exhibited a stronger distance-decay relationship than the satellite sub-communities. In addition, topological properties of nodes in the network demonstrated that the core sub-communities had more complex and stable co-occurrence associations and were primarily driven by stochastic processes (58.19%). By contrast, the satellite sub-communities were mainly governed by deterministic processes (62.17%). Overall, this study demonstrated the differences in the core and satellite sub-community assembly and network stability, suggesting the importance of considering species traits to understand the biogeographic distribution of bacterial communities in high-altitude lakes.

Responses of Arbuscular Mycorrhizal Fungi Diversity and Community to 41-Year Rotation Fertilization in Brown Soil Region of Northeast China

Arbuscular mycorrhizal fungi (AMF) play vital roles in the growth and development of plants, ecosystem sustainability, and stability in agroecosystem, such as transporting nutrients to host plants, improving soil physical structure, and enhancing the stress resistance of host plants. However, the effects of fertilization on AMF diversity and community in brown soil areas are still unclear. The purpose of this study is to explore changes in AMF diversity and community structures and finding out the factors that influenced the changes after 41 years of fertilization in brown soil. Samples were collected from five treatments of the long-term fertilization experiment in June 2019, including CK (no fertilizer), N (mineral nitrogen fertilizer), NP (mineral nitrogen and phosphate fertilizer), M (pig manure), and MNP (pig manure, mineral nitrogen, and phosphate fertilizer). Illumina HiSeq sequencing was used to determine AMF diversity and community structure. The relationship between AMF communities in soil and roots and environmental factors was analyzed by redundancy analysis. The results showed that the soil nutrient content of manure treatments was generally higher than that of chemical fertilizer treatments and no fertilizer treatment. Long-term fertilization increased AMF spore density, which increased with the increase of soil fertility. The moderate content of soil available phosphorus was beneficial to the colonization of AMF. AMF diversity in soil decreased with soil fertility, but AMF diversity in roots was influenced only by soil nitrate–nitrogen and pH. Glomus was the dominant genus in both soil and root samples. AMF community structure in soil and roots had a different response to long-term fertilization. Application of manure had a greater impact on AMF community structure in soil, whereas application of exogenous phosphate fertilizer had a greater impact on that in roots. Soil ammonium nitrogen, nitrate–nitrogen, total nitrogen, organic carbon, total potassium, and available potassium were the most important factors that influenced taxa of AMF in soil, whereas soil ammonium nitrogen, nitrate–nitrogen, total nitrogen, organic carbon, total potassium, available potassium, available phosphorus, and plant phosphorus and potassium content were the most important factors influencing taxa of AMF in maize roots under long-term fertilization in brown soil.

Core and occasional species: A new way forward

Various methods have been used to divide communities into core species and occasional or satellite species. Some methods are somewhat arbitrary, and there is evidence that many communities are more multimodal than bimodal. They also tend to rely on having multiple years of data.A completely novel method is presented that not only has no requirement for long-term datasets but can divide communities into multiple groups. It is based on probability a species is present, calculated using Simpson's index and the sequential removal of species from the data.The sequential Simpson's index method was applied to species data from a grassland insect community. It was also applied to eleven other datasets that had been divided into core and occasional species in previously published studies.The new method was found not only to be consistent with previous core-occasional assessments but also able to identify multimodality in species abundance distributions.Although ideally used with a measure of persistence (frequency of occurrence) to rank species, community structure is consistently described even with only species abundance data.The method can be applied to short or long-term datasets and can help identify multimodality and provide valuable insight into how communities change in time or space.

Strong impact of micropollutants on prokaryotic communities at the horizontal but not vertical scales in a subtropical reservoir, China

Micropollutants have become of great concern, because of their disrupting effects on the structure and function of microbial communities. However, little is known about the relative importance of trace micropollutants on the aquatic prokaryotic communities as compared to the traditional physico-chemical characteristics, especially at different spatial dimensions. Here, we investigated free-living (FL) and particle-associated (PA) prokaryotic communities in a subtropical water reservoir, China, across seasons at horizontal (surface water) and vertical (depth-profile) scales by using 16S rRNA gene amplicon sequencing. Our results showed that the shared variances of physico-chemicals and micropollutants explained majority of the spatial variations in prokaryotic communities, suggesting a strong joint effect of the two abiotic categories on reservoir prokaryotic communities. Micropollutants appeared to exert strong independent influence on the core sub-communities (i.e., abundant and wide-spread taxa) than on the satellite (i.e., less abundant and narrow-range taxa) counterparts. The pure effect of micropollutants on both core and satellite sub-communities from FL and PA fractions was ~1.5 folds greater than that of physico-chemical factors at the horizontal scale, whereas an opposite effect was observed at the vertical scale. Moreover, eight micropollutants including anti-fungal agents, antibiotics, bisphenol analogues, stimulant and UV-filter were identified as the major disrupting compounds with strong associations with core taxa of typical freshwater prokaryotes. Altogether, we concluded that the ecological disrupting effects of micropollutants on prokaryotic communities may vary along horizontal and vertical dimensions in freshwater ecosystems.

Unraveling spatiotemporal variability of arbuscular mycorrhizal fungi in a temperate grassland plot

Soils provide a heterogeneous environment varying in space and time; consequently, the biodiversity of soil microorganisms also differs spatially and temporally. For soil microbes tightly associated with plant roots, such as arbuscular mycorrhizal fungi (AMF), the diversity of plant partners and seasonal variability in trophic exchanges between the symbionts introduce additional heterogeneity. To clarify the impact of such heterogeneity, we investigated spatiotemporal variation in AMF diversity on a plot scale (10 × 10 m) in a grassland managed at low intensity in southwest Germany. AMF diversity was determined using 18S rDNA pyrosequencing analysis of 360 soil samples taken at six time points within a year. We observed high AMF alpha- and beta-diversity across the plot and at all investigated time points. Relationships were detected between spatiotemporal variation in AMF OTU richness and plant species richness, root biomass, minimal changes in soil texture and pH. The plot was characterized by high AMF turnover rates with a positive spatiotemporal relationship for AMF beta-diversity. However, environmental variables explained only ≈20% of the variation in AMF communities. This indicates that the observed spatiotemporal richness and community variability of AMF was largely independent of the abiotic environment, but related to plant properties and the cooccurring microbiome.

Deciphering the Assembly Processes of the Key Ecological Assemblages of Microbial Communities in Thirteen Full-Scale Wastewater Treatment Plants

Limited information is currently available on the assembly processes (deterministic vs. stochastic) shaping the compositions of key microbial communities in activated sludge (AS). The relative importance of deterministic and stochastic processes for key bacterial and archaeal assemblages (i.e., core-satellite and habitat generalist-specialist) in AS from 13 wastewater treatment plants in China was investigated using 16S rDNA amplicon sequencing. The results obtained indicated 1,388 and 369 core operational taxonomic units (OTUs), 1,038 and 1,683 satellite OTUs, 255 and 48 habitat generalist OTUs, and 192 and 111 habitat specialist OTUs for Bacteria and Archaea, respectively. The proportions of shared OTUs between core and habitat specialist communities were similar to or higher than those between core and habitat generalist communities, suggesting a stronger inter-linkage between the former two groups. Deterministic processes, indicated by abundance-based β-null models, were responsible for shaping core communities, in which NH₄-N, OrgC/OrgN, Cr, and Ni were the main controlling factors. In contrast, satellite communities were predominantly influenced by stochastic processes. Moreover, we found that deterministic and stochastic processes were mainly responsible for shaping the assembly of habitat specialists and generalists, respectively. However, the influence of deterministic factors on habitat specialists remains unclear. The present study provides novel insights into the assembly mechanisms of AS microbial communities.

Extreme rainfall affects assembly of the root-associated fungal community

Global warming is resulting in increased frequency of weather extremes. Root-associated fungi play important roles in terrestrial biogeochemical cycling processes, but the way in which they are affected by extreme weather is unclear. Here, we performed long-term field monitoring of the root-associated fungus community of a short rotation coppice willow plantation, and compared community dynamics before and after a once in 100 yr rainfall event that occurred in the UK in 2012. Monitoring of the root-associated fungi was performed over a 3-yr period by metabarcoding the fungal internal transcribed spacer (ITS) region. Repeated soil testing and continuous climatic monitoring supplemented community data, and the relative effects of environmental and temporal variation were determined on the root-associated fungal community. Soil saturation and surface water were recorded throughout the early growing season of 2012, following extreme rainfall. This was associated with a crash in the richness and relative abundance of ectomycorrhizal fungi, with each declining by over 50%. Richness and relative abundance of saprophytes and pathogens increased. We conclude that extreme rainfall events may be important yet overlooked determinants of root-associated fungal community assembly. Given the integral role of ectomycorrhizal fungi in biogeochemical cycles, these events may have considerable impacts upon the functioning of terrestrial ecosystems.

Seasonal variation in winter wheat field soil arbuscular mycorrhizal fungus communities after non-mycorrhizal crop cultivation

Intensive farming practices that implement deep and frequent tillage, high input inorganic fertilization, cultivation with non-host species, and pesticide use are widely reported to be detrimental for arbuscular mycorrhizal fungi (AMF), which are one of the most important plant biofertilizers. The effect of the reduction of agricultural input on AMF community dynamics following conversion from conventional non-mycorrhizal to lower input mycorrhizal crop cultivation has not yet been fully elucidated. We investigated the effect of the reduction of agricultural input, rotation, and season on AMF communities in winter wheat field soil after conversion from long-term (more than 20 years) non-mycorrhizal (sugar beet) crop cultivation. We described AMF communities from bulk soil samples by specifically targeting the 18S ribosomal gene using a combination of AMF specific primers and 454 pyrosequencing. No effect was found after 3 years' reduction of agricultural input, and only marginal effects were due to rotation with specific crops preceding winter wheat. Instead, season and year of sampling had the most appreciable influence on the AMF community. We suggest that, after conversion from long-term non-mycorrhizal to mycorrhizal crop cultivation, AMF diversity is low if compared to similar agroecosystems. Seasonal and successional dynamics play an important role as determinants of community structure.

Compost Addition Enhanced Hyphal Growth and Sporulation of Arbuscular Mycorrhizal Fungi without Affecting Their Community Composition in the Soil

Arbuscular mycorrhizal (AM) fungi form symbiotic associations with most crop plant species in agricultural ecosystems, and are conspicuously influenced by various agricultural practices. To understand the impact of compost addition on AM fungi, we examined effect of four compost rates (0, 11.25, 22.5, and 45 Mg/ha) on the abundance and community composition of AM fungi in seedling, flowering, and mature stage of soybean in a 1-year compost addition experiment system in Northeast China. Soybean [Glycine max (L.) Merrill] was used as test plant. Moderate (22.5 Mg/ha) and high (45 Mg/ha) levels of compost addition significantly increased AM root colonization and extraradical hyphal (ERH) density compared with control, whereas low (11.5 Mg/ha) level of compost addition did not cause significant increase in AM root colonization and ERH density. AM fungal spore density was significantly enhanced by all the compost rates compared with control. The temporal variations analysis revealed that, AM root colonization in seedling stage was significantly lower than in flowering and mature stage. Although AM fungal operational taxonomic unit richness and community composition was unaffected by compost addition, some abundant AM fungal species showed significantly different response to compost addition. In mature stage, Rhizophagus fasciculatum showed increasing trend along with compost addition gradient, whereas the opposite was observed with Paraglomus sp. In addition, AM fungal community composition exhibited significant temporal variation during growing season. Further analysis indicated that the temporal variation in AM fungal community only occurred in control treatment, but not in low, moderate, and high level of compost addition treatments. Our findings highlighted the significant effects of compost addition on AM growth and sporulation, and emphasized that growth stage is a stronger determinant than 1-year compost addition in shaping AM fungal community in black soil of Northeast China.