Plastisphere microbiome: Methodology, diversity, and functionality.

Broad topics of the plastisphere in various environments are reviewed, including its methodologies, diversity, functionality, and outlook.

Automated identification and quantification of invisible microplastics in agricultural soils.

Microplastics in agricultural soils have become the research hotspot in recent years, however, the quantitative methods based on the traditional visual inspection may have a high false detection rate. Here we combined the laser direct infrared (LDIR) and Fourier-transform infrared (FTIR) methods to investigate the microplastics in farmland with long-term agricultural activities. The results showed that the total abundance of microplastics reached 1.98 ± 0.41 × 105, 1.57 ± 0.28 × 105, 1.78 ± 0.27 × 105, and 3.20 ± 0.41 × 105 particles/kg soil in cotton fields with film mulching of 5, 10, 20, and >30 years, respectively. LDIR results indicated that microplastics ranging from 10 to 500 µm accounted for 96.5-99.9 % of the total microplastic amounts in the soils. Additionally, a total of 26 polymer types of microplastics were detected, among which polyethylene (PE), polypropylene (PP), polyvinyl chloride (PVC), polyamide (PA), and polytetrafluoroethylene (PTFE) were dominantly observed. For the microplastics detected by FTIR (500 µm-5 mm), PE polymer was majorly observed (88.0-98.9 %). Most microplastics were films (88.2 %), while fibers and pellets were also found. The reclaimed water from sewage treatment plants, the drip irrigation utilities, and the residual plastic film are the potential sources of microplastics in the farmland soils. By using the automated quantitative and identifiable approaches, this study suggested that the commonly used visual counting method may underestimate the microplastic contamination in agricultural soils.

Dissolved organic matter (DOM) quality drives biogeographic patterns of soil bacterial communities and their association networks in semi-arid regions.

It is of great interest to elucidate the biogeographic patterns of soil microorganisms and their driving forces, which is fundamental to predicting alterations in microbial-mediated functions arising from environment changes. Although dissolved organic matter (DOM) represents an important resource for soil microorganisms, knowledge of how its quality affects microbial biogeography is limited. Here, we characterized soil bacterial communities and DOM quality in 45 soil samples collected from a 1500-km sampling transect through semi-arid regions in northern China which are currently suffering great pressure from climate change, using Illumina Miseq sequencing and fluorescence spectroscopy, respectively. We found that DOM quality (i.e. the source of DOM and the humification degree of DOM) had profound shaping influence on the biogeographic patterns exhibited by bacterial diversity, community composition and association networks. Specifically, the composition of bacteria community closely associated with DOM quality. Plant-derived DOM sustained higher bacterial diversity relative to microbial-derived DOM. Meanwhile, bacterial diversity linearly increased with increasing humification degree of DOM. Additionally, plant-derived DOM was observed to foster more complex bacterial association networks with less competition. Together, our work contributes to the factors underlying biogeographic patterns not only of bacterial diversity, community composition but also of their association networks and reports previously undocumented important role of DOM quality in shaping these patterns.

Spatial Patterns of Soil Fungal Communities Are Driven by Dissolved Organic Matter (DOM) Quality in Semi-Arid Regions.

Soil fungi are ecologically important as decomposers, pathogens, and symbionts in nature. Understanding their biogeographic patterns and driving forces is pivotal to predict alterations arising from environmental changes in ecosystem. Dissolved organic matter (DOM) is an essential resource for soil fungi; however, the role of its quality in structuring fungal community patterns remains elusive. Here using Illumina MiSeq sequencing, we characterized total fungi and their functional groups in 45 soil samples collected from a 1500-km sampling transect through semi-arid regions in northern China, which are currently suffering great pressure from climate change. Total fungi and their functional groups were all observed to exhibit significant biogeographic patterns which were primarily driven by environmental variables. DOM quality was the best and consistent predictor of diversity of both total fungi and functional groups. Specifically, plant-derived DOM was associated with greater diversity relative to microbe-dominated origins. In addition, fungal diversity linearly increased with increases in degree of humification in DOM. Similarly, among all measured environmental variables, DOM quality had the strongest effects on the community composition of total fungi and functional groups. Together, our work contributes to the factors underlying fungal biogeographic patterns and adds detail to the importance of DOM quality in structuring fungal communities.

Deciphering the archaeal communities in tree rhizosphere of the Qinghai-Tibetan plateau.

BACKGROUND: The Qinghai-Tibetan Plateau represents one of the most important component of the terrestrial ecosystem and a particularly vulnerable region, which harbouring complex and diverse microbiota. The knowledge about their underground microorganisms have largely been studied, but the characteristics of rhizosphere microbiota, particularly archaeal communities remains unclear. RESULTS: High-throughput Illumina sequencing was used to investigate the rhizosphere archaeal communities of two native alpine trees (Picea crassifolia and Populus szechuanica) living on the Qinghai-Tibetan Plateau. The archaeal community structure in rhizospheres significantly differed from that in bulk soil. Thaumarchaeota was the dominant archaeal phylum in all soils tested (92.46-98.01%), while its relative abundance in rhizospheres were significantly higher than that in bulk soil. Ammonium nitrogen, soil organic matter, available phosphorus and pH were significantly correlated with the archaeal community structure, and the deterministic processes dominated the assembly of archaeal communities across all soils. In addition, the network structures of the archaeal community in the rhizosphere were less complex than they were in the bulk soil, and an unclassified archaeal group (Unclassified_k_norank) was identified as the keystone species in all archaeal networks. CONCLUSIONS: Overall, the structure, assembly and co-occurrence patterns of archaeal communities are significantly affected by the presence of roots of alpine trees living on the Qinghai-Tibetan Plateau. This study provides new insights into our understanding of archaeal communities in vulnerable ecosystems.

LDPE microplastics significantly alter the temporal turnover of soil microbial communities.

Although the ubiquitous presence of microplastics in various environments is increasingly well studied, knowledge of the effects of microplastics on ambient microbial communities is still insufficient. To estimate the response of soil bacterial community succession and temporal turnover to microplastic amendment, a soil microcosm experiment was carried out with polyethylene microplastics. The soil samples under control and microplastic amendment conditions were collected for sequencing analysis using Illumina MiSeq technology. Microplastic amendment was found to significantly alter soil bacterial community structure, and the community differences were increased linearly with the incubation time. Compared with the turnover rate of bacterial community in the control samples (0.0103, p < .05, based on Bray-Curtis similarity), the succession rate was significantly (p < .001) higher in the soil with microplastic amendment (0.0309, p < .001). In addition, the effects of microplastic amendment on the time-decay relationships (TDRs) on taxonomic divisions revealed considerable variations of TDRs values, indicating the effects were lineage dependent. Our results propose that the presence of microbial in soil ecosystem may lead to a faster succession rate of soil bacterial community, which provides new insights into the evolutionary consequences of microplastics in terrestrial environment.

Microplastics from mulching film is a distinct habitat for bacteria in farmland soil.

Microplastics, as an emerging pollutant of global importance, have been well documented in aquatic ecosystems. However, little is known about the effects of microplastics on agroecosystems, particularly for soil microbial communities. Herein, microplastics collected from cotton fields in Xinjiang, China, were analysed with a scanning electron microscope (SEM) and high-throughput sequencing to investigate the attached bacterial communities. Microplastic surfaces, especially pits and flakes, were colonized by various microorganisms, suggesting active hydrolysis of plastic debris. The bacterial communities colonizing microplastics were significantly different in structure from those in the surrounding soil, plant litter and macroplastics. In addition, statistical analysis of differentially abundant OTUs showed that microplastics serve as a "special microbial accumulator" in farmland soil, enriching some taxa that degrade polyethylene, such as Actinobacteria, Bacteroidetes and Proteobacteria. Co-occurrence network analysis revealed that the biotic interactions between microorganisms on microplastics are as complex as those in soil, and Acidobacteria, Chloroflexi, Gemmatimonadetes, and Bacteroidetes are considered keystone species in bacterial communities. Collectively, the findings imply that microplastics acted as a distinct habitat for bacteria in farmland soil, which increases our understanding of microplastic pollution.

Potential metal-binding ability of proteins in the extracellular slime of Laccaria bicolor exposed to excessive Cu and Cd.

Ectomycorrhizal fungi can enhance the tolerance of plants to heavy metal stress by reducing the accumulation of heavy metals in the aerial parts of the plants. Extracellular chelation is a major mechanism of heavy metal tolerance in ectomycorrhizal fungi in which extracellular slime plays a fundamental role. The objectives of this study were to investigate the potential metal-binding ability and the protein composition of extracellular slime. The extracellular slime of Laccaria bicolor (L. bicolor) cultivated under Cd2+ and Cu2+ stress was separated using various ultrasonic pre-treatments. The protein content, composition, and metal content of the extracellular slime were measured. The results showed that the protein content in the extracellular slime significantly increased under both Cd2+ and Cu2+ stress. The SDS-PAGE profile showed that Cd2+ and Cu2+ stress induced the expression of several new proteins. Heavy metal quantification revealed that the Cd content fixed in the extracellular slime accounted for 22-28% of the metal fixed by the fungal mycelia. Meanwhile, no Cu was detected in the fungal extracellular slime, implying that the extracellular slime may not be effective for the fixation of essential metallic elements such as Cu. Taken together, these results provided evidence that L. bicolor was able to ameliorate the intracellular Cd content by stimulating extracellular slime exudation and altering the composition of the proteins therein. Nevertheless, this blocking strategy may be effective only for the non-essential element Cd and was ineffective for the physiological element Cu.

Increasing aridity affects soil archaeal communities by mediating soil niches in semi-arid regions.

Soil archaea plays a vital role in the functioning of dryland ecosystems, which are expected to expand and get drier in the future as a result of climate change. However, compared with bacteria and fungi, the impacts of increasing aridity on archaea in these ecosystems remain largely unknown. Here, soil samples were collected along a typical aridity gradient in semi-arid regions in Inner Mongolia, China, to investigate whether and how the increasing aridity affects archaeal communities. The results showed that archaeal richness linearly decreased with increasing aridity. After partialling out the effects of soil properties based on partial least squares regression, the significant aridity-richness relationship vanished. The composition of archaeal communities was distributed according to the aridity gradient. These variations were largely driven by the changes in the relative abundance of Thaumarchaeota, Euryarchaeota and unclassified phyla. Niche-based processes were predominant in structuring the observed archaeal aridity-related pattern. The structural equation models further showed that aridity indirectly reduced archaeal richness through improving soil electrical conductivity (EC) and structured community composition by changing soil total nitrogen (TN). These results suggested that soil salinization and N-losses might be important mechanisms underlying the increasing aridity-induced alterations in archaeal communities, and highlighted the importance of soil niches in mediating the indirect impacts of increasing aridity on archaea.

Urbanization altered regional soil organic matter quantity and quality: Insight from excitation emission matrix (EEM) and parallel factor analysis (PARAFAC).

Soil organic matter (SOM) play an important role in soil ecology and global carbon dynamic. As one of the most sever and irreversible land use change, urbanization could alter the regional carbon storage and composition pattern. However how urbanization influence on SOM is still unclear. In this study, we collected soil samples from highly urbanized area of Beijing, China and explore the quantity and quality variations of SOM by using fluorescence spectroscopy in combine with parallel factor analysis (PARAFAC). The results shown that the soil physic-chemical properties were shaped by urbanization. Comparing to nature soil, moisture content, total organic carbon and total nitrogen in urban and rural soil significantly decreased. The fluorescence spectrum demonstrated that SOM quality was also altered by urbanization induced environmental changes. Five fluorescent compounds in SOM was identified by PARAFAC model and three of them was assigned to humic-like substances. The fluorescence intensity of humic-like substances in nature land was significantly higher than of rural and urban land, meanwhile microbial related substance accumulated in urban land in comparison with rural and nature land. The multivariate analyses further reveal the relationship between soil physic-chemical properties and SOM composition. These results suggest that urbanization could not only decrease the SOM quantity but also change the SOM composition. The SOM loss caused by urbanization was mainly consist of humic-like substance loss. Besides urbanization also stimulate the accumulation of microbial related substance in SOM which highlight the importance of microorganism is SOM dynamic.