Dynamics of microbial biomass and community composition after short-term water status change in Chinese paddy soils

Effects of different sizes of microplastic particles on soil respiration, enzyme activities, microbial communities, and seed germination

Microplastics (MPs) are emerging pollutants of terrestrial ecosystems. The impacts of MP particle size on terrestrial systems remain unclear. The current study aimed to investigate the effects of six particle sizes (i.e., 4500, 1500, 500, 50, 5, and 0.5 μm) of polyethylene (PE) and polyvinyl chloride (PVC) on soil respiration, enzyme activity, bacteria, fungi, protists, and seed germination. MPs significantly promoted soil respiration, and the stimulating effects of PE were the strongest for medium and small-sized (0.5-1500 μm) particles, while those of PVC were the strongest for small particle sizes (0.5-50 μm). Large-sized (4500 μm) PE and all sizes of PVC significantly improved soil urease activity, while medium-sized (1500 μm) PVC significantly improved soil invertase activity. MPs altered the soil microbial community diversity, and the effects were especially pronounced for medium and small-sized (0.5-1500 μm) particles of PE and PVC on bacteria and fungi and small-sized (0.5 μm) particles of PE on protists. The impacts of MPs on bacteria and fungi were greater than on protists. The seed germination rate of Brassica chinensis decreased gradually with the decrease in PE MPs particle size. Therefore, to reduce the impact of MPs on soil ecosystems, effective measures should be taken to avoid the transformation of MPs into smaller particles in soil environmental management.

Herbicide application impacted soil microbial community composition and biochemical properties in a flooded rice field

Herbicide application is a common practice in intensive agriculture. However, accumulating herbicide residues in the ecosystem affects important soil attributes. The effect of two herbicides, pendimethalin and pretilachlor, on soil biochemical properties and microbial community composition was studied in a transplanted paddy field. Results reveal a gradual decline in herbicide residue up to 60 days after application. Changes in soil microbiological and biochemical properties (microbial biomass, enzymes, respiration, etc.) showed an inconsistent pattern across the treatments. Quantitative polymerase chain reaction analysis showed the archaeal, bacterial and fungal populations to be of higher order in control soil compared to the treated one. Amplicon sequencing (16S rRNA and ITS genes) exhibited that besides the unclassified genera, ammonia-oxidizing Crenarchaeota and the group represented by Candidatus Nitrososphaera were dominant in both the control and treated samples. Other archaeal genera viz. Methanosarcina and Bathyarchaeia showed a slight decrease in relative abundance of control (0.5 %) compared to the treated soil (0.7 %). Irrespective of treatments, the majority of bacterial genera comprised unclassified and uncultured species, accounting for >64-75 % in the control group and over 78.29 % in the treated samples. Members of Vicinamibacteraceae, Bacillus and Bryobacter were dominant in control samples. Dominant fungal genera belonging to unclassified groups comprised Curvularia, Aspergillus, and Emericellopsis in the control group, whereas Paraphysoderma and Emericellopsis in the herbicide-treated groups. Inconsistent response of soil properties and microbial community composition is evident from the present study, suggesting that the recommended dose of herbicides might not result in any significant change in microbial community composition. The findings of this investigation will help in the formulation of a framework for risk assessment and maintaining sustainable rice cultivation in herbicide- amended soils.

Oyster aquaculture enhances sediment microbial diversity- Insights from a multi-omics study

The global aquaculture industry has grown substantially, with consequences for coastal ecology and biogeochemistry. Oyster aquaculture can alter the availability of resources for microbes that live in sediments as oysters move large quantities of organic material to the sediments via filter feeding, possibly leading to changes in the structure and function of sediment microbial communities. Here, we use a chronosequence approach to investigate the impacts of oyster farming on sediment microbial communities over 7 years of aquaculture activity in a temperate coastal system. We detected shifts in bacterial composition (16S rRNA amplicon sequencing), changes in gene expression (meta-transcriptomics), and variations in sediment elemental concentrations (sediment geochemistry) across different durations of oyster farming. Our results indicate that both the structure and function of bacterial communities vary between control (no oysters) and farm sites, with an overall increase in diversity and a shift towards anoxic tolerance in farm sites. However, little to no variation was observed in either structure or function with respect to farming duration suggesting these sediment microbial communities are resilient to change. We also did not find any significant impact of farming on heavy metal accumulation in the sediments. The minimal influence of long-term oyster farming on sediment bacterial function and biogeochemical processes as observed here can bear important consequences for establishing best practices for sustainable farming in these areas.

Importance

Sediment microbial communities drive a range of important ecosystem processes such as nutrient recycling and filtration. Oysters are well-known ecological engineers, and their presence is increasing as aquaculture expands in coastal waters globally. Determining how oyster aquaculture impacts sediment microbial processes is key to understanding current and future estuarine biogeochemical processes. Here, we use a multi-omics approach to study the effect of different durations of oyster farming on the structure and function of bacteria and elemental accumulation in the farm sediments. Our results indicate an increase in the diversity of bacterial communities in the farm sites with no such increases observed for elemental concentrations. Further, these effects persist across multiple years of farming with an increase of anoxic tolerant bacteria at farm sites. The multi-omics approach used in this study can serve as a valuable tool to facilitate understanding of the environmental impacts of oyster aquaculture.

Effects of soil habitat changes on antibiotic resistance genes and related microbiomes in paddy fields

The changes of paddy soil habitat profoundly affect the structure and function of soil microorganisms, but how this process drives the growth and spread of manure- derived antibiotic resistance genes (ARGs) after entering the soil is unclear. Herein, this study explored the environmental fate and behavior of various ARGs in the paddy soil during rice growth period. Results showed that most ARG abundances in flooded soil was lower than that in non-flooded soil during rice growth (decreased by 33.4 %). And soil dry-wet alternation altered microbial community structure in paddy field (P < 0.05), showing that Actinobacteria and Firmicutes increased in proportion under non-flooded conditions, and Chloroflexi, Proteobacteria and Acidobacteria evolved into the dominant groups in flooded soil. Meanwhile, the correlation between ARGs and bacterial communities was stronger than that with mobile genetic elements (MGEs) in both flooded and non-flooded paddy soils. Furthermore, soil properties, especially oxidation reduction potential (ORP), were proved to be an essential factor in regulating the variability of ARGs in the whole rice growth stage by structural equation model, with a direct influence (λ = 0.38, P < 0.05), following by similar effects of bacterial communities and MGEs (λ = 0.36, P < 0.05; λ = 0.29, P < 0.05). This study demonstrated that soil dry-wet alternation effectively reduced the proliferation and dissemination of most ARGs in paddy fields, providing a novel agronomic measure for pollution control of antibiotic resistance in farmland ecosystem.

Comprehensive improvement of soil quality and rice yield by flooding-midseason drying-flooding

Many water-saving technologies have been developed to reduce water input and the associated irrigation costs. However, the influence of water management technologies on soil quality is unclear. Soil quality is fundamental to rice yield and sustainable productivity of ecosystems. Therefore, it is important to understand the effect of water management on soil quality and its linkage with rice yield. In this work, a field experiment was conducted to assess the influence of water management on soil physico-chemical properties, microbial biomass, bacterial community, and rice yield in paddy fields. Three water treatments were selected for the study, including flooding-rain-fed (F-RF), flooding-midseason drying-flooding (F-D-F), and continuous flooding (CF). Total nitrogen (TN), total phosphorus (TP), dissolved carbon content (DOC), available phosphorus (AP), nitrate nitrogen (NO₃^-), microbial biomass carbon (MBC), and microbial biomass nitrogen (MBN) contents were 11%, 20%, 29%, 30%, 11%, 183%, and 215% higher in F-D-F, respectively, than those in the CF (p < 0.05). Additionally, the bacterial diversity in F-D-F and CF was significantly higher compared to the F-RF (p < 0.05). Correspondingly, soil quality index (SQI) was higher in the F-D-F (0.8) than that of F-RF (0.53) and CF (0.5). Compared with the F-RF, water management remarkably altered bacterial community composition, with higher enrichment of anaerobic bacteria (such as Firmicutes and Chloroflexi) in flooding treatments (CF and F-D-F). Differences in the bacterial community were closely related to key soil quality indicators, such as AP. Parallel increases in soil quality and bacterial diversity resulted in increased rice yield in the F-D-F, which was 53% and 12% higher than that in F-RF and CF, respectively. Therefore, F-D-F is the suggested water management method because it can comprehensively improve soil microbial diversity, soil quality, and rice yield. KEY POINTS: • Water management changed bacterial community mainly via SMC (soil moisture content), TP, AP, and NO₃^-contents. • The F-D-F had greater SQI and higher rice yield in comparison with F-RF and CF.

Microbial retention and resistances in stormwater quality improvement devices treating road runoff

Current knowledge about the microbial communities that occur in urban road runoff is scarce. Road runoff of trafficked roads can be heavily polluted and is treated by stormwater quality improvement devices (SQIDs). However, microbes may influence the treatment process of these devices or could lead to stress resistant opportunistic microbial strains. In this study, the microbial community in the influent, effluent and the filter materials used to remove dissolved heavy metals from two different SQIDs were analyzed to determine microbial load, retention, composition, and mobile resistance genes. Although the microbes were replaced by new taxa in the effluent, there was no major retention of microbial genera. Further, the bacterial abundance of the SQIDs effluent was relatively stable over time. The heavy metal content correlated with intl1 and with microbial genera. The filter media itself was enriched with Intl1 gene cassettes, carrying several heavy metal and multidrug resistance genes (e.g. czrA, czcA, silP, mexW and mexI), indicating that this is a hot spot for horizontal gene transfer. Overall, the results shed light on road runoff microbial communities, and pointed to distinct bacterial communities within the SQIDs, which subsequently influence the microbial community and the genes released with the treated water.

Similar but Not Identical Resuscitation Trajectories of the Soil Microbial Community Based on Either DNA or RNA after Flooding

Both drought and flooding are unfavorable for soil microorganisms, but nevertheless, are highly relevant to the extreme weather events that have been predicted to increase in the future. The switch of soil water status from drought to flooding can happen rapidly and microbial activity might be either stimulated or further inhibited, but we have insufficient understanding of the underlying microbial processes. Here, we tracked the changes in soil bacterial and fungal abundance and their community structures, assaying the total (DNA-based) and potentially active (RNA-based) communities in response to abrupt flooding of dry soil. Also, rates of soil respiration and enzyme activity were measured after flooding. Results showed that the bacterial community was found to be more responsive than the fungal community to flooding. The bacterial community responses were clearly classified into three distinct patterns in which the intermediate pattern displayed highly phylogenetic clustering. A transient flourish of Bacilli which belongs to Firmicutes was detected at 8–48 h of flooding, suggesting its potential importance in the microbial assemblage and subsequent ecosystem functioning. Finally, the accumulative amount of CO2 released was more closely related than enzyme activity to the change in structure of the bacterial community after flooding. In conclusion, these findings extended our understanding of the underlying soil microbial processes following abrupt water condition changes.

Land Use and Seasonal Effects on the Soil Microbiome of a Brazilian Dry Forest

Drylands occupy approximately 41% of the Earth's terrestrial surface. Climate change and land use practices are expected to affect biogeochemical cycling by the soil microbiome in these ecosystems. Understanding how soil microbial community might respond to these drivers is extremely important to mitigate the processes of land degradation and desertification. The Caatinga, an exclusively Brazilian biome composed of an extensive seasonal tropical dry forest, is exposed to variable spatiotemporal rainfall patterns as well as strong human-driven pressures. Herein, an integrated analysis of shotgun metagenomics approach coupled to meteorological data was employed to unravel the impact of seasonality and land use change on soil microbiome from preserved and agriculture-affected experimental fields in Caatinga drylands. Multivariate analysis suggested that microbial communities of preserved soils under seasonal changes were shaped primarily by water deficit, with a strong increase of Actinobacteria and Proteobacteria members in the dry and rainy seasons, respectively. In contrast, nutrient availability notably played a critical role in driving the microbial community in agriculture-affected soils. The strong enrichment of bacterial genera belonging to the poorly-known phylum Acidobacteria ('Candidatus Solibacter' and 'Candidatus Koribacter') in soils from dry season affected by ferti-irrigation practices presupposes a contrasting copiotrophic lifestyle and ecological role in mitigating the impact of chemical fertilization. Functional analyses identify overrepresented genes related to osmotic stress response (synthesis of osmoprotectant compounds, accumulation of potassium ions) and preferential carbon and nitrogen utilization when comparing the microbiome of preserved soils under seasonal changes, reflecting differences in the genetic potential for nutrient cycling and C acquisition in the environment. However, the prevalence of nitrosative stress and denitrification functions in irrigation/fertilization-affected soils of the dry season clearly suggest that nutrient input and disruption of natural water regime may impact biogeochemical cycles linked to the microbial processes, with potential impacts on the ecosystem functionality. These findings help to better understand how natural seasonality and agricultural management differentially affect soil microbial ecology from dry forests, providing support for the development of more sustainable land management in dryland ecosystems.

Assessment of Microbial Community Dynamics in River Bank Filtrate Using High-Throughput Sequencing and Flow Cytometry

Surface-groundwater interactions play an important role in microbial community compositions of river bank filtrates. Surface water contaminations deriving from environmental influences are attenuated by biogeochemical processes in the hyporheic zone, which are essential for providing clean and high-quality drinking water in abstraction wells. Characterizing the flow regime of surface water into the groundwater body can provide substantial information on water quality, but complex hydraulic dynamics make predictions difficult. Thus, a bottom up approach using microbial community shifting patterns as an overall outcome of dynamic water characteristics could provide more detailed information on the influences that affect groundwater quality. The combination of high-throughput sequencing data together with flow cytometric measurements of total cell counts reveals absolute abundances among taxa, thus enhancing interpretation of bacterial dynamics. 16S rRNA high-throughput sequencing of 55 samples among six wells in a well field in Austria that is influenced by river bank filtrate within a time period of 3 months has revealed both, clear differences as well as strong similarity in microbiome compositions between wells and dates. A significant community shift from April to May occurred in four of six wells, suggesting that surface water flow regimes do affect these wells stronger than others. Triplicate sampling and subsequent sequencing of wells at different dates proved the method to be reproducible. Flow cytometric measurements of total cells indicate microbial shifts due to increased cell counts and emphasize the rise of allochthonous microorganisms. Typical freshwater bacterial lineages (Verrucomicrobia, Bacteroidetes, Actinobacteria, Cyanobacteria, Armatimonadetes) were identified as most increasing phyla during community shifts. The changes are most likely a result of increased water abstraction in the wells together with constant river water levels rather than rain events. The results provide important knowledge for future implementations of well utilization in dependency of the nearby Danube River water levels and can help drawing conclusions about the influence of surface water in the groundwater such that hygienically save and clean drinking water with a stable microbial community can be provided.