Viral and bacterial community responses to stimulated Fe(III)-bioreduction during simulated subsurface bioremediation

Influence of iron (hydr)oxide mineralogy and contents in aquifer sediments on dissolved organic carbon attenuations during aquifer storage and recovery

Aquifer storage and recovery (ASR) is a promising approach for managing water resources that enhances water quality through biogeochemical reactions occurring within aquifers. Iron (hydr)oxides, which are the predominant metallic oxides in soil, play a crucial role in degrading dissolved organic carbon (DOC), primarily through a process known as dissimilatory iron reduction (DIR). However, the efficiency of this reaction varies depending on the mineralogy and composition of the aquifer, and this understanding is essential for adequate water quality in ASR. The objective of this study is to investigate the impact of iron (hydr)oxide on acetate, as an organic carbon source, attenuation during the ASR. To achieve this, three sets of laboratory sediment columns were prepared, each containing a different type of iron (hydr)oxide minerals: ferrihydrite, goethite, and hematite. Following an acclimation period of 28 days to simulate the microcosm within an aquifer, the columns were continuously supplied with the simulated river water spiked with acetate (DOC 40-60 mg L-1), and the acetate concentration in the effluent was monitored. The result revealed that the column containing ferrihydrite achieved 97% acetate attenuation through DIR with anoxic conditions (DO < 0.1 mg L-1), while the goethite and hematite columns exhibited limited attenuation rates of 40 and 50%, respectively. Furthermore, the efficiency of acetate attenuation in the ferrihydrite columns increased with the content of ferrihydrite but experienced a rapidly declined at higher contents (3-4%), possibly due to the partial conversion of ferrihydrite to goethite as a result of the interaction between ferrihydrite and the Fe(II) produced during DIR. Additionally, an analysis of the microbial community demonstrated that microorganisms known to possess the ability to reduce iron (hydr)oxides under anaerobic conditions were abundant in the ferrihydrite columns.

Effects of Fe(III) (hydr)oxide mineralogy on the development of microbial communities originating from soil, surface water, groundwater, and aerosols

Microbial Fe(III) reduction is a key component of the iron cycle in natural environments. However, the susceptibility of Fe(III) (hydr)oxides to microbial reduction varies depending on the mineral's crystallinity, and the type of Fe(III) (hydr)oxide in turn will affect the composition of the microbial community. We created microcosm reactors with microbial communities from four different sources (soil, surface water, groundwater, and aerosols), three Fe(III) (hydr)oxides (lepidocrocite, goethite, and hematite) as electron acceptors, and acetate as an electron donor to investigate the shaping effect of Fe(III) mineral type on the development of microbial communities. During a 10-month incubation, changes in microbial community composition, Fe(III) reduction, and acetate utilization were monitored. Overall, there was greater reduction of lepidocrocite than of goethite and hematite, and the development of microbial communities originating from the same source diverged when supplied with different Fe(III) (hydr)oxides. Furthermore, each Fe(III) mineral was associated with unique taxa that emerged from different sources. This study illustrates the taxonomic diversity of Fe(III)-reducing microbes from a broad range of natural environments.

Viral lysing can alleviate microbial nutrient limitations and accumulate recalcitrant dissolved organic matter components in soil

Viruses are critical for regulating microbial communities and biogeochemical processes affecting carbon/nutrient cycling. However, the role of soil phages in controlling microbial physiological traits and intrinsic dissolved organic matter (DOM) properties remains largely unknown. Herein, microcosm experiments with different soil phage concentrates (including no-added phages, inactive phages, and three dilutions of active phages) at two temperatures (15 °C and 25 °C) were conducted to disclose the nutrient and DOM dynamics associated with viral lysing. Results demonstrated three different phases of viral impacts on CO2 emission at both temperatures, and phages played a role in maintaining Q10 within bounds. At both temperatures, microbial nutrient limitations (especially P limitation) were alleviated by viral lysing as determined by extracellular enzyme activity (decreased Vangle with active phages). Additionally, the re-utilization of lysate-derived DOM by surviving microbes stimulated an increase of microbial metabolic efficiency and recalcitrant DOM components (e.g., SUV254, SUV260 and HIX). This research provides direct experimental evidence that the "viral shuttle" exists in soils, whereby soil phages increase recalcitrant DOM components. Our findings advance the understanding of viral controls on soil biogeochemical processes, and provide a new perspective for assessing whether soil phages provide a net "carbon sink" vs. "carbon source" in soils.

Accumulation of nitrite after reclaimed water recharge due to the disinfection byproduct chlorite

Due to its toxicity, the disinfection byproduct chlorite in drinking water is strictly regulated to be ≤ 1.0 mg/L, but in reclaimed, non-drinking water chlorite is unregulated and rarely considered. However, chlorite is cytotoxic and has a high oxidation potential. Therefore, as reclaimed water infiltrates soil and groundwater, it may alter the soil environment and microbial community, which may affect the degradation of organic matter and the transformation of the N element. In this study, the effects of reclaimed water containing chlorite on soil microorganisms were investigated by simulating subsurface infiltration. It was found that chlorite improved the conversion of nitrate nitrogen to nitrite nitrogen, but inhibited further conversion of nitrite nitrogen. The nitrite nitrogen in the effluent reached 4.61 mg/L when chlorite was present, while only 0.16 mg/L was found in the control system. The chlorite produced obvious oxidative stress reactions in cells, inhibited the EPSs production, in which the contents of polysaccharides and proteins reduced by nearly 41% and 62%, respectively. Besides, chlorite resulted in the enrichment of efflux resistance genes in the microbial community, mainly adeF and cmlB1. Self-protection against chlorite is achieved mainly using efflux pump related genes. Metagenomics data analysis showed that Delftia became the dominant genus when exposed to chlorite, with the greatest abundance at 17.9%. Chlorite also resulted in the upregulated expression of nar genes (by more than 149%) and downregulation of nir gene expression (by more than 62%). This study reveals the effects of the disinfection byproduct chlorite on a soil microecosystem, providing important information for the management and reuse of reclaimed water.

Biogeographical Patterns and Assembly of Bacterial Communities in Saline Soils of Northeast China

Increasing salinity undermines soil fertility and imposes great threats to soil ecosystem productivity and ecological sustainability. Microbes with the ability to adapt to environmental adversity have gained increasing attention for maintenance and restoration of the salt-affected soil ecosystem structure and functioning; however, the characterization of microbial communities in saline–sodic soils remains limited. This study characterized the bacterial community composition and diversity in saline–sodic soils along a latitude gradient across Northeast China, aiming to reveal the mechanism of physicochemical and geographic characteristics shaping the soil bacterial communities. Our results showed that the bacterial community composition and diversity were significantly impacted by soil pH, electrical conductivity, Na⁺, K⁺, Cl⁻, and CO₃²⁻. Significant differences in bacterial diversity were revealed along the latitude gradient, and the soil factors accounted for 58.58% of the total variations in bacterial community composition. Proteobacteria, Actinobacteria, Gemmatimonadetes, Chloroflexi, and Bacteroidetes were dominant across all samples. Actinobacteria and Gemmatimonadetes were significantly enriched in high soil sodicity and salinity, while Acidobacteria and Proteobacteria were suppressed by high pH and salt stress in the saline–sodic soils. Increase in soil pH and salinity significantly decreased bacterial species richness and diversity. Community composition analysis indicated that bacterial taxonomic groups (e.g., Bacillus, Egicoccus, Truepera, Halomonas, and Nitrolancea) that may adapt well to high salinity were greatly enriched in the examined soils. The findings collectively evidenced that bacterial community composition and diversity in a broad biographic scale were determined by niche-based environmental characteristics and biotic interactions. The profiling of the soil bacterial communities along the latitude gradient will also provide a basis for a better understanding of the salt-affected soil ecosystem functioning and restoration of these soil ecosystems.

Microbial biomass and activity dynamics in restored lands in a metal contaminated region

Soil microbial communities are important for biogeochemical processes, along with the cycling of nutrients in an ecosystem. Their enzymatic activities are key indicators of their responses to stress. The objective of this research was to assess the effect of land reclamation on microbial biomass and activities in soils impacted by metal contamination. Phospholipid fatty acid analysis (PLFA) (PLFA) results revealed a significant increase in total microbial biomass, fungi, actinomycetes, and bacteria when limed soils were compared to unlimed samples. This change in microbial biomass was associated with a significant increase of pH. The overall level of the β-glucosidase (BG), cellobiohydrolase (CBH), and aryl sulfatase (AS) activities was significantly higher in the dolomitic limestone treated soils than in the untreated samples. However, the activity of glycine aminopeptidase (GAP) was significantly lower in the limed soil than in unlimed samples used as reference. No significant differences (P ≥ 0.05) were observed between the two types of lands (limed vs unlimed) for other enzymes tested, which includes β-N-acetylglucosaminidase (NAGase), acid phosphatase (AP), alkaline phosphatase (ALP), leucine aminopeptidase (LAP), and peroxidase (PER). The levels of enzymatic responses also varied among sites. Overall, this study revealed for the first time the effects of liming on soil microbial activities in recently reclaimed sites damaged by metals.

Phage strategies facilitate bacterial coexistence under environmental variability

Bacterial communities are often exposed to temporal variations in resource availability, which exceed bacterial generation times and thereby affect bacterial coexistence. Bacterial population dynamics are also shaped by bacteriophages, which are a main cause of bacterial mortality. Several strategies are proposed in the literature to describe infections by phages, such as "Killing the Winner", "Piggyback the loser" (PtL) or "Piggyback the Winner" (PtW). The two temperate phage strategies PtL and PtW are defined by a change from lytic to lysogenic infection when the host density changes, from high to low or from low to high, respectively. To date, the occurrence of different phage strategies and their response to environmental variability is poorly understood. In our study, we developed a microbial trophic network model using ordinary differential equations (ODEs) and performed 'in silico' experiments. To model the switch from the lysogenic to the lytic cycle, we modified the lysis rate of infected bacteria and their growth was turned on or off using a density-dependent switching point. We addressed whether and how the different phage strategies facilitate bacteria coexistence competing for limiting resources. We also studied the impact of a fluctuating resource inflow to evaluate the response of the different phage strategies to environmental variability. Our results show that the viral shunt (i.e. nutrient release after bacterial lysis) leads to an enrichment of the system. This enrichment enables bacterial coexistence at lower resource concentrations. We were able to show that an established, purely lytic model leads to stable bacterial coexistence despite fluctuating resources. Both temperate phage models differ in their coexistence patterns. The model of PtW yields stable bacterial coexistence at a limited range of resource supply and is most sensitive to resource fluctuations. Interestingly, the purely lytic phage strategy and PtW both result in stable bacteria coexistence at oligotrophic conditions. The PtL model facilitates stable bacterial coexistence over a large range of stable and fluctuating resource inflow. An increase in bacterial growth rate results in a higher resilience to resource variability for the PtL and the lytic infection model. We propose that both temperate phage strategies represent different mechanisms of phages coping with environmental variability. Our study demonstrates how phage strategies can maintain bacterial coexistence in constant and fluctuating environments.

Bacteriophage-host depth distribution patterns in soil are maintained after nutrient stimulation in vitro

Previous research has revealed the ecological importance of viruses in different ecosystems. However, bacteriophage-host distribution patterns in soil depth profiles have not been investigated. Environmental factors such as nutrient availability and physiological stress can impact the mode (either lytic or lysogenic) of viral reproduction and subsequent influence of virus infection on ecological processes. Soil depth profiles with distinct geochemical properties are ideal models to investigate the virus-host relationships as a function of environmental trophic status and cell abundance. Batch enrichment experiments using soil collected at varying depths (0-140 cm) as inoculum were performed to explore the interactions between viruses and co-occurring microbial hosts under nutrient stimulation. Both viral and bacterial abundance increased in the nutrient media compared with those in the original soils. Bacterial abundance was similar in mixed-cultures of soils regardless of sampling depth, whereas viral abundance was negatively correlated with the depth of soil samples which caused a decreasing virus-to-bacteria ratio. The lysogenetic fraction increased with soil depth in a similar manner as in the original soils assessed directly without nutrient stimulation. The bacterial diversity decreased with soil depth, and was influenced primarily by soil type, viral abundance, and virus-to-bacteria ratio. The bacterial communities were dominated by Bacilli, Beta-, Gamma-Proteobacteria, and Clostridia after nutrient stimulation. Viral and bacterial community structure also varied with soil horizons (i.e., depth). The results showed that the patterns for virus-host interactions shaped by the geochemical properties in the original environment were conserved or similar after in vitro nutrient stimulation. These findings suggest that short-term changes in trophic status alone may not significantly alter the balance of viral reproductive strategies in terrestrial ecosystems as in the antecedent environmental conditions that the host community has long adapted to, and other factors such as stress, host diversity or adaptation may be necessary to trigger community-level shifts in the interactions between viruses and hosts that responded most favorably to nutrient addition.

Improvement of Soil Microbial Diversity through Sustainable Agricultural Practices and Its Evaluation by -Omics Approaches: A Perspective for the Environment, Food Quality and Human Safety

Soil is one of the key elements for supporting life on Earth. It delivers multiple ecosystem services, which are provided by soil processes and functions performed by soil biodiversity. In particular, soil microbiome is one of the fundamental components in the sustainment of plant biomass production and plant health. Both targeted and untargeted management of soil microbial communities appear to be promising in the sustainable improvement of food crop yield, its nutritional quality and safety. –Omics approaches, which allow the assessment of microbial phylogenetic diversity and functional information, have increasingly been used in recent years to study changes in soil microbial diversity caused by agronomic practices and environmental factors. The application of these high-throughput technologies to the study of soil microbial diversity, plant health and the quality of derived raw materials will help strengthen the link between soil well-being, food quality, food safety and human health.

Toluene Bioremediation by Using Geotextile-Layered Permeable Reactive Barriers (PRBs)

Sources of contamination in a subsurface environment are petrol, diesel fuel, gasoline at oil refineries, underground storage tanks, transmission pipelines, and different industries. The permeable reactive barrier (PRB) is a promising technology to remediate groundwater in-situ. In this study, synthetic groundwater samples containing toluene are treated in three reactor columns by biological processes. PRB-1 consisted of sand and gravel as reactor media, microbial inoculum (bioaugmentation—BA), and nutrients (biostimulation—BS); PRB-2 consisted of sand and gravel as reactor media, microbial inoculum, nutrients, and 12 layers of nonwoven geotextile fabrics; and PRB-3 consisted of only sand and gravel as reactor media (natural attenuation—NA). This study was conducted to assess the impact of geotextile fabric filter, bioaugmentation, and biostimulation on toluene degradation efficiency. After 167 days of treatment, toluene biodegradation efficiencies varied between 88.2% and 93.8% for PRB 1, between 98.0% and 99.3% for PRB 2, and between 14.2% and 68.6% for PRB 3. The effluent toluene concentrations for PRB-2 were less than the guideline value (0.7 mg/L) of the World Health Organization. Reaction rate data were fitted with a first-order kinetic reaction rate model. This study showed that the toluene removal efficiency in the geotextile layered PRB combined with BA and BS process was significantly higher compared to the other processes tested. This lab-scale study introduced a new PRB configuration suitable for the remediation of sites contaminated with toluene.

Viral Abundance and Diversity of Production Fluids in Oil Reservoirs

Viruses are widely distributed in various ecosystems and have important impacts on microbial evolution, community structure and function and nutrient cycling in the environment. Viral abundance, diversity and distribution are important for a better understanding of ecosystem functioning and have often been investigated in marine, soil, and other environments. Though microbes have proven useful in oil recovery under extreme conditions, little is known about virus community dynamics in such systems. In this study, injection water and production fluids were sampled in two blocks of the Daqing oilfield limited company where water flooding and microbial flooding were continuously used to improve oil recovery. Virus-like particles (VLPs) and bacteria in these samples were extracted and enumerated with epifluorescence microscopy, and viromes of these samples were also sequenced with Illumina Hiseq PE150. The results showed that a large number of viruses existed in the oil reservoir, and VLPs abundance of production wells was 3.9 ± 0.7 × 10⁸ mL^-1 and virus to bacteria ratio (VBR) was 6.6 ± 1.1 during water flooding. Compared with water flooding, the production wells of microbial flooding had relative lower VLPs abundance (3.3 ± 0.3 × 10⁸ mL^-1) but higher VBR (7.9 ± 2.2). Assembled viral contigs were mapped to an in-house virus reference data separate from the GenBank non-redundant nucleotide (NT) database, and the sequences annotated as virus accounted for 35.34 and 55.04% of total sequences in samples of water flooding and microbial flooding, respectively. In water flooding, 7 and 6 viral families were identified in the injection and production wells, respectively. In microbial flooding, 6 viral families were identified in the injection and production wells. The total number of identified viral species in the injection well was higher than that in the production wells for both water flooding and microbial flooding. The Shannon diversity index was higher in the production well of water flooding than in the production well of microbial flooding. These results show that viruses are very abundant and diverse in the oil reservoir's ecosystem, and future efforts are needed to reveal the potential function of viral communities in this extreme environment.

Temporal Dynamics of Soil Virus and Bacterial Populations in Agricultural and Early Plant Successional Soils

As reported in many aquatic environments, recent studies in terrestrial ecosystems implicate a role for viruses in shaping the structure, function, and evolution of prokaryotic soil communities. However, given the heterogeneity of soil and the physical constraints (i.e., pore-scale hydrology and solid-phase adsorption of phage and host cells) on the mobility of viruses and bacteria, phage-host interactions likely differ from those in aquatic systems. In this study, temporal changes in the population dynamics of viruses and bacteria in soils under different land management practices were examined. The results showed that bacterial abundance was significantly and positively correlated to both virus and inducible prophage abundance. Bacterial and viral abundance were also correlated with soil organic carbon and nitrogen content as well as with C:N ratio. The seasonal variability in viral abundance increased with soil organic carbon content. The prokaryotic community structure was influenced more by land use than by seasonal variation though considerable variation was evident in the early plant successional and grassland sites. The free extracellular viral communities were also separated by land use, and the forest soil viral assemblage exhibiting the most seasonal variability was more distinct from the other sites. Viral assemblages from the agricultural soils exhibited the least seasonal variability. Similar patterns were observed for inducible prophage viral assemblages. Seasonal variability of viral assemblages was greater in mitomycin-C (mitC) induced prophages than in extracellular viruses irrespective of land use and management. Taken together, the data suggest that soil viral production and decay are likely balanced but there was clear evidence that the structure of viral assemblages is influenced by land use and by season.

Quorum Sensing Signals Alter in vitro Soil Virus Abundance and Bacterial Community Composition

Cell-density dependent quorum sensing (QS) is fundamental for many coordinated behaviors among bacteria. Most recently several studies have revealed a role for bacterial QS communication in bacteriophage (phage) reproductive decisions. However, QS based phage-host interactions remain largely unknown, with the mechanistic details revealed for only a few phage-host pairs and a dearth of information available at the microbial community level. Here we report on the specific action of eight different individual QS signals (acyl-homoserine lactones; AHLs varying in acyl-chain length from four to 14 carbon atoms) on prophage induction in soil microbial communities. We show QS autoinducers, triggered prophage induction in soil bacteria and the response was significant enough to alter bacterial community composition in vitro. AHL treatment significantly decreased the bacterial diversity (Shannon Index) but did not significantly impact species richness. Exposure to short chain-length AHLs resulted in a decrease in the abundance of different taxa than exposure to higher molecular weight AHLs. Each AHL targeted a different subset of bacterial taxa. Our observations indicate that individual AHLs may trigger prophage induction in different bacterial taxa leading to changes in microbial community structure. The findings also have implications for the role of phage-host interactions in ecologically significant processes such as biogeochemical cycles, and phage mediated transfer of host genes, e.g., photosynthesis and heavy metal/antibiotic resistance.

Dynamics of Bacterial and Viral Communities in Paddy Soil with Irrigation and Urea Application

Viruses are ubiquitous in natural systems. By influencing bacterial abundance (BA) and community structure through lysis-lysogenic conversion, viruses are involved in various ecological processes. In agricultural management, nitrogen addition and irrigation should be considered as important factors that can modify soil viral dynamics but have been ignored. In our study, short-term dynamics of autochthonous soil viral and bacterial abundance and diversity after irrigation and urea application were examined in a long-term experimental paddy field. Urea addition delayed the emergence of peak viral abundance for three days, suggesting that viruses are sensitive to N addition. Under short-term eutrophic conditions through urea application, viruses undertake a lysogenic-biased strategy. Moreover, nitrogen-fixing bacteria were most likely specifically lysed in urea-treated soil, which suggests that soil viruses block N accumulation by killing nitrogen-fixing bacteria. To the best of our knowledge, this study is the first to investigate dynamic changes in autochthonous viruses in paddy fields.