Molecular and Dual-Isotopic Profiling of the Microbial Controls on Nitrogen Leaching in Agricultural Soils under Managed Aquifer Recharge.

Nitrate (NO3-) leaching is a serious health and ecological concern in global agroecosystems, particularly those under the application of agricultural-managed aquifer recharge (Ag-MAR); however, there is an absence of information on microbial controls affecting NO3- leaching outcomes. We combine natural dual isotopes of NO3- (15N/14N and 18O/16O) with metagenomics, quantitative polymerase chain reaction (PCR), and a threshold indicator taxa analysis (TITAN) to investigate the activities, taxon profiles, and environmental controls of soil microbiome associated with NO3- leaching at different depths from Californian vineyards under Ag-MAR application. The isotopic signatures demonstrated a significant priming effect (P < 0.01) of Ag-MAR on denitrification activities in the topsoil (0-10 cm), with a 12-25-fold increase of 15N-NO3- and 18O-NO3- after the first 24 h of flooding, followed by a sharp decrease in the enrichment of both isotopes with ∼80% decline in denitrification activities thereafter. In contrast, deeper soils (60-100 cm) showed minimal or no denitrification activities over the course of Ag-MAR application, thus resulting in 10-20-fold of residual NO3- being leached. Metagenomic profiling and laboratory microcosm demonstrated that both nitrifying and denitrifying groups, responsible for controlling NO3- leaching, decreased in abundance and potential activity rates with soil depth. TITAN suggested that Nitrosocosmicus and Bradyrhizobium, as the major nitrifier and denitrifier, had the highest and lowest tipping points with regard to the NO3- changes (P < 0.05), respectively. Overall, our study provides new insight into specific depth limitations of microbial controls on soil NO3- leaching in agroecosystems.

Plant invasion reconstructs soil microbial assembly and functionality in coastal salt marshes.

Microbiologically driven ecosystem processes can be profoundly altered by alien plant invasions. There is limited understanding of the ecological mechanisms orchestrating different microbial constituents and their roles in emerging functional properties under plant invasions. Here, we investigated soil microbial communities and functions using high-throughput amplicon sequencing and GeoChip technology, respectively, along a chronological gradient of smooth cordgrass invasion in salt marshes located in the Yellow River Estuary, China. We found a positive correlation between microbial diversity and the duration age of invasion, and both bacterial and fungal communities showed consistent changes with invasion. Soil microbial metabolic potential, as indicated by the abundance of microbial functional genes involved in biogeochemical cycling, decreased in response to invasion. As a consequence, declining soil microbial metabolisms as a result of plant invasion facilitated carbon accumulation in invaded salt marshes. Bacteria and fungi exhibited distinct contributions to assembly processes along the invasion gradient: bacterial communities were mainly driven by selection and dispersal limitation, while fungi were dramatically shaped by stochastic processes. Soil microbial-mediated functions were taxon-specific, as indicated by community-function relationships. This study demonstrates the distinct contributions of microbial constituents to microbial community assembly and functions and sheds light on the implications of plant invasion on microbiologically driven ecosystem processes in coastal wetlands.

Habitat-specific responses of soil organic matter decomposition to Spartina alterniflora invasion along China's coast.

Plant invasions cause a fundamental change in soil organic matter (SOM) turnover. Disentangling the biogeographic patterns and key drivers of SOM decomposition and its temperature sensitivity (Q10 ) under plant invasion is a prerequisite for making projections of global carbon feedback. We collected soil samples along China's coast across saltmarshes to mangrove ecosystems invaded by the smooth cordgrass (Spartina alterniflora Loisel.). Microcosm experiments were carried out to determine the patterns of SOM decomposition and its thermal response. Soil microbial biomass and communities were also characterized accordingly. SOM decomposition constant dramatically decreased along the mean annual temperature gradient, whereas the cordgrass invasion retarded this change (significantly reduced slope, p < 0.05). The response of Q10 to invasion and the soil microbial quotient peaked at midlatitude saltmarshes, which can be explained by microbial metabolism strategies. Climatic variables showed strong negative controls on the Q10 , whereas dissolved carbon fraction exerted a positive influence on its spatial variance. Higher microbial diversity appeared to weaken the temperature-related response of SOM decomposition, with apparent benefits for carbon sequestration. Inconsistent responses to invasion were exhibited among habitat types, with SOM accumulation in saltmarshes but carbon loss in mangroves, which were explained, at least in part, by the SOM decomposition patterns under invasion. This study elucidates the geographic pattern of SOM decomposition and its temperature sensitivity in coastal ecosystems and underlines the importance of interactions between climate, soil, and microbiota for stabilizing SOM under plant invasion.

Campylobacterota dominate the microbial communities in a tropical karst subterranean estuary, with implications for cycling and export of nitrogen to coastal waters.

Subterranean estuaries (STEs), the zones in which seawater and subsurface groundwater mix, are recognized as hotspots for biogeochemical reactions; however, little is known of the microbial communities that control many of those reactions. This study investigated the potential functions of microbes inhabiting a cenote and an offshore submarine spring (Pargos) in the near-coastal waters of the Yucatan Peninsula, Mexico. The inland cenote (Cenote Siete Bocas; C7B) is characterized by a chemocline that is host to an array of physicochemical gradients associated with microbial activities. The chemocline includes an increasing gradient in sulfide concentrations with depth and a decreasing gradient in nitrate concentrations. The microbial community within the chemocline was dominated by Sulfurimonas and Sulfurovum of the Campylobacteria, which are likely responsible for sulfide oxidation coupled with nitrate reduction. Although C7B has not been directly connected with Pargos Spring, water discharging from the spring has physicochemical characteristics and microbial community structures similar to C7B, strongly suggesting biogeochemical processing in the STE impacts groundwater composition prior to discharge. This work yields insight into the microbial communities and biogeochemical reactions in STEs in karstic aquifers and provides evidence for the importance of Campylobacteria in controlling nitrate concentrations exported to marine springs.

Microbial resistance and resilience in response to environmental changes under the higher intensity of human activities than global average level.

With the increasing intensity of global human activities, the ecosystem function, which is supported by the microbial community, will be dramatically changed and impaired. To investigate microbial resistance and resilience of microbial communities to human activities, we chose two typical types of human disturbances, urbanization, and reclamation under the higher intensity of human activities than the global average level. We examined microbial traits, including the abundance, diversity, phylogeny, and co-occurrence interactions in soil microbial communities, together with the nitrification activities observed in the subtropical coastal ecosystem of the Pearl River Estuary and in soil microcosm experiments. Microbial communities were less resistant to the environmental changes caused by urbanization than to those caused by reclamation, which was significantly reflected in the nitrogen and/or carbon-related patterns. However, most of the microbial traits could be recovered almost to the original level without significant differences in the microcosm after 40 days of incubation. The co-occurrence interactions between nitrifiers and other microbial communities were dramatically changed and could not be completely recovered, but this change did not affect their nitrification activities for balancing the ammonium in the soil to the original level during the recovery stage, suggesting that the interactions between microbial communities might have fewer effects on their activities than previously thought. This study quantitatively demonstrated that microbial communities as a whole can recover to a status similar to the original state in a short time after the removal of stress at a large ecosystem scale even under the higher intensity of human activities than global average level in coastal ecosystems, which implied a strong recovery capacity of soil microbial community even after intense human disturbance.

Microbiota recovery in a chronosquences of impoverished Cerrado soils with biosolids applications.

Mining activities put the Brazilian savannas, a global biodiversity hotspot, in danger of species and soil carbon losses. Experiments employing biosolids have been applied to rejuvenate this degraded ecosystem, but a lingering question yet to be answered is whether the microbiota that inhabits these impoverished soils can be recovered towards its initial steady state after vegetation recovery. Here, we selected an 18-year-old restoration chronosequence of biosolids-treated, untreated mining and native soils to investigate the soil microbiota recovery based on composition, phylogeny, and diversity, as well as the potential factors responsible for ecosystem recovery. Our results revealed that the soil microbiota holds a considerable recovery potential in the degraded Cerrado biome. Biosolids application not only improved soil health, but also led to 41.7 % recovery of the whole microbial community, featuring significantly higher microbiota diversity and enriched groups (e.g., Firmicutes) that benefit carbon storage compared to untreated mining and native soils. The recovered community showed significant compositional distinctions from the untreated mining or native soils, rather than phylogenetic differences, with physiochemical properties explaining 55 % of the overall community changes. This study advances our understanding of soil microbiota dynamics in response to disturbance and restoration by shedding light on its recovery associated with biosolid application in a degraded biodiverse ecosystem.

Grazing exclusion-induced changes in soil fungal communities in a highly desertified Brazilian dryland.

Soil desertification poses a critical ecological challenge in arid and semiarid climates worldwide, leading to decreased soil productivity due to the disruption of essential microbial community processes. Fungi, as one of the most important soil microbial communities, play a crucial role in enhancing nutrient and water uptake by plants through mycorrhizal associations. However, the impact of overgrazing-induced desertification on fungal community structure, particularly in the Caatinga biome of semiarid regions, remains unclear. In this study, we assessed the changes in both the total fungal community and the arbuscular mycorrhizal fungal community (AMF) across 1. Natural vegetation (native), 2. Grazing exclusion (20 years) (restored), and 3. affected by overgrazing-induced degradation (degraded) scenarios. Our assessment, conducted during both the dry and rainy seasons in Irauçuba, Ceará, utilized Internal Transcribed Spacer (ITS) gene sequencing via Illumina® platform. Our findings highlighted the significant roles of the AMF families Glomeraceae (∼71% of the total sequences) and Acaulosporaceae (∼14% of the total sequences) as potential key taxa in mitigating climate change within dryland areas. Moreover, we identified the orders Pleosporales (∼35% of the total sequences) and Capnodiales (∼21% of the total sequences) as the most abundant soil fungal communities in the Caatinga biome. The structure of the total fungal community differed when comparing native and restored areas to degraded areas. Total fungal communities from native and restored areas clustered together, suggesting that grazing exclusion has the potential to improve soil properties and recover fungal community structure amid global climate change challenges.

Distribution and pollution, toxicity and risk assessment of heavy metals in sediments from urban and rural rivers of the Pearl River delta in southern China.

Sediments were collected from the upper, middle and lower reaches of both urban and rural rivers in a typical urbanization zone of the Pearl River delta. Six heavy metals (Cd, Cr, Cu, Ni, Pb and Zn) were analyzed in all sediment samples, and their spatial distribution, pollution levels, toxicity and ecological risk levels were evaluated to compare the characteristics of heavy metal pollution between the two rivers. Our results indicated that the total contents of the six metals in all samples exceeded the soil background value in Guangdong province. Based on the soil quality thresholds of the China SEPA, Cd levels at all sites exceeded class III criteria, and other metals exhibited pollution levels exceeding class II or III criteria at both river sites. According to the sediment quality guidelines of the US EPA, all samples were moderately to heavily polluted by Cr, Cu, Ni, Pb and Zn. Compared to rural river sites, urban river sites exhibited heavier pollution. Almost all sediment samples from both rivers exhibited moderate to serious toxicity to the environment, with higher contributions from Cr and Ni. A "hot area" of heavy metal pollution being observed in the upper and middle reaches of the urban river area, whereas a "hot spot" was identified at a specific site in the middle reach of the rural river. Contrary metal distribution patterns were also observed along typical sediment profiles from urban and rural rivers. However, the potential ecological risk indices of rural river sediments in this study were equal to those of urban river sediments, implying that the ecological health issues of the rivers in the undeveloped rural area should also be addressed. Sediment organic matter and grain size might be important factors influencing the distribution profiles of these heavy metals.

Nitrogen fate during agricultural managed aquifer recharge: Linking plant response, hydrologic, and geochemical processes.

Agricultural managed aquifer recharge (Ag-MAR, on-farm recharge), where farmland is flooded with excess surface water to intentionally recharge groundwater, has received increasing attention by policy makers and researchers in recent years. However, there remain concerns about the potential for Ag-MAR to exacerbate nitrate (NO3-) contamination of groundwater, and additional risks, such as greenhouse gas emissions and crop tolerance to prolonged flooding. Here, we conducted a large-scale, replicated winter groundwater recharge experiment to quantify the effect of Ag-MAR on soil N biogeochemical transformations, potential NO3- leaching to groundwater, soil physico-chemical conditions, and crop yield. The field experiment was conducted in two grapevine vineyards in the Central Valley of California, which were each flooded for 2 weeks and 4 weeks, respectively, with 1.31 and 1.32 m3 m-2 of water. Hydrologic, geochemical, and microbial results indicate that NO3- leaching from the first 1 m of the vadose zone was the dominant N loss pathway during flooding. Based on pore water sample and N2O emission data, denitrification played a lesser role in decreasing NO3- in the root zone but prolonged anoxic conditions resulted in a significant 29 % yield decrease in the 4-week flooded vineyard. The results from this research, combined with data from previous studies, are summarized in a new conceptual model for integrated water-N dynamics under Ag-MAR. The proposed model can be used to determine best Ag-MAR management practices.

Nitrogen and phosphorous acquisition strategies drive coexistence patterns among archaeal lineages in soil.

Soil represents the largest reservoir of Archaea on Earth. Present-day archaeal diversity in soils globally is dominated by members of the class Nitrososphaeria. The evolutionary radiation of this class is thought to reflect adaptations to a wide range of temperatures, pH, and other environmental conditions. However, the mechanisms that govern competition and coexistence among Nitrososphaeria lineages in soil remain poorly understood. Here we show that predominant soil Nitrososphaeria lineages compose a patchwork of gene inventory and expression profiles for ammonia, urea, and phosphate utilization. In contrast, carbon fixation, respiration, and ATP synthesis genes are conserved and expressed consistently among predominant phylotypes across 12 major evolutionary lineages commonly found in soil. In situ gene expression profiles closely resemble pure culture reference strains under optimal growth conditions. Together, these results reveal resource-based coexistence patterns among Nitrososphaeria lineages and suggest complementary ecophysiological niches associated with differential nutrient acquisition strategies among globally predominant archaeal lineages in soil.

Ammonia-oxidizing archaea are integral to nitrogen cycling in a highly fertile agricultural soil.

Nitrification is a central process in the global nitrogen cycle, carried out by a complex network of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), complete ammonia-oxidizing (comammox) bacteria, and nitrite-oxidizing bacteria (NOB). Nitrification is responsible for significant nitrogen leaching and N2O emissions and thought to impede plant nitrogen use efficiency in agricultural systems. However, the actual contribution of each nitrifier group to net rates and N2O emissions remain poorly understood. We hypothesized that highly fertile agricultural soils with high organic matter mineralization rates could allow a detailed characterization of N cycling in these soils. Using a combination of molecular and activity measurements, we show that in a mixed AOA, AOB, and comammox community, AOA outnumbered low diversity assemblages of AOB and comammox 50- to 430-fold, and strongly dominated net nitrification activities with low N2O yields between 0.18 and 0.41 ng N2O-N per µg NOx-N in cropped, fallow, as well as native soil. Nitrification rates were not significantly different in plant-covered and fallow plots. Mass balance calculations indicated that plants relied heavily on nitrate, and not ammonium as primary nitrogen source in these soils. Together, these results imply AOA as integral part of the nitrogen cycle in a highly fertile agricultural soil.

Effects of magnetic biochar-microbe composite on Cd remediation and microbial responses in paddy soil.

There is growing global interest in the bioremediation of cadmium (Cd) using combinations of biochar and microorganisms. However, the interactions among biochar, introduced and indigenous microorganisms remain unclear. Accordingly, a 90 day microcosm experiment was conducted to investigate this by adding Bacillus sp. K1 strain inoculated rice straw biochar (SBB) and magnetic straw biochar (MBB) into a Cd contaminated paddy soil from Hunan, China. All treatments were incubated aerobically (60% water holding capacity) or anaerobically for 90 d. During both soil incubations, Bacillus sp. K1 successfully colonized in soil with composites applications. Soil pH was significantly increased from acid to neutral, and available Cd decreased with the addition of both composites. The better remediation efficiency of MBB than SBB under anerobic conditions was attributed to the transformation of acetic acid-extractable Cd into the residual fraction, caused by Cd2+ bonding with crystal Fe3O4. The application of the two kinds of composites caused similar changes to both microbial communities. There was a slight decrease in indigenous microbial alpha diversity with the MBB aerobic application, while the total population number of bacteria was increased by 700%. Both the redundancy analysis and Mantel analyses indicated that pH and microbial biomass C contributed to the colonization of Bacillus sp. K1 with SBB under aerobic conditions, and with MBB under anerobic conditions, respectively. The research provides a new insight into interactive effects and investigates immobilization mechanisms involved of bacterial/biochar composites in anaerobic and aerobic soils.

Desalinization via freshwater restoration highly improved microbial diversity, co-occurrence patterns and functions in coastal wetland soils.

Saltwater intrusion has greatly impacted the functions of coastal wetland soils worldwide by increasing the salt stress; desalinization via freshwater restoration has been suggested to recover saline wetland soils and biodiversity, but its effectiveness is debated. To evaluate the desalinization effectiveness, we characterized the microbial communities and activities using high throughput 16S rRNA gene sequencing and 15N isotopic techniques in freshwater restored (≥10 years) and unrestored wetlands, and then compared the data with reported values of original freshwater wetlands in one of the most dynamic coastal areas, Yellow river estuary (YRE). Our data revealed that freshwater input significantly increased the soil organic carbon (SOC; P < 0.05) after 10 years of restoration, yet it was still 10 times lower than the reported values of original freshwater wetlands. In general, microbial community showed higher diversities and more co-occurrence interactions in the restored than unrestored wetlands. The recovered phylogenetic diversity and the relative abundance of Chloroflexi (9.8-16.3%), Actinobacteria (5.5-10%), Latescibacteria (0.5-1.5%), Nitrospirae (0.9-1.4%) were up to the similar levels of original freshwater wetlands in YRE. Specifically, Gemmatimonadetes_denitrifier clones, as the representatives of denitrifiers, were recovered up to 0.3% with 20 times higher concomitant denitrification rate than anammox rate, significantly contributing to the nitrate removal in restored wetlands; however the rate will be reduced by 80% with a short-term saltwater intrusion. Our study highlighted that freshwater input effectively improved the microbial diversity and their functions and provided a good insight into the desalinization effectiveness via freshwater restoration in coastal wetlands worldwide. ORIGINALITY-SIGNIFICANCE STATEMENT: Salinization is globally spreading with approximately one billion hectares area covered with saline and/or sodic soils on the earth, and the negative effects of salinity on soil microbial communities and their activities have been frequently reported in previous studies all around the world; however, it remains largely unknown about whether the microbial communities and their activities can be recovered or not in soil suffered salinization. Desalinization via freshwater restoration is supposed to offer a good solution to soil salinization in coastal area, but the effectiveness is debated. Here, we are presenting the long-term of field study related to the desalinization effects on microbial diversity, co-occurrence and functions, and find desalinization via freshwater restoration can recover most of microbial communities up to the similar levels of that in original freshwater wetlands, and highly improved microbial diversity and their functions, which sheds a positive light on soil desalinization via freshwater restoration at microenvironments.

Spartina alterniflora invasions reduce soil fungal diversity and simplify co-occurrence networks in a salt marsh ecosystem.

Soil fungal communities drive diverse ecological processes and are critical in maintaining ecosystems' stability, but the effects of plant invasion on soil fungal diversity, community composition, and functional groups are not well understood. Here, we investigated soil fungal communities in a salt marsh ecosystem with both native (Suaeda salsa) and exotic (Spartina alterniflora) species in the Yellow River Delta. We characterized fungal diversity based on the PCR-amplified Internal Transcribed Spacer 2 (ITS2) DNA sequences from soil extracted total DNA. The plant invasion evidently decreased fungal richness and phylogenetic diversity and significantly altered the taxonomic community composition (indicated by the permutation test, P < 0.001). Co-occurrence networks between fungal species showed fewer network links but were more assembled because of the high modularity after the invasion. As indicated by the fungal Bray-Curtis and weighted UniFrac distances, the fungal community became homogenized with the invasion. FUNGuild database analyses revealed that the invaded sites had a higher proportion of saprophytic fungi, suggesting higher organic matter decomposition potential with the invasion. The plant invasion dramatically inhibited the growth of pathogenic fungi, which may facilitate the expansion of invasive plants in the intertidal habitats. Soil pH and salinity were identified as the most important edaphic factors in shaping the fungal community structures in the context of Spartina alterniflora invasion. Overall, this study elucidates the linkage between plant invasion and soil fungal communities and poses potential consequences for fungal contribution to ecosystem function, including the decomposition of soil organic substrates.

Response of microbial populations regulating nutrient biogeochemical cycles to oiling of coastal saltmarshes from the Deepwater Horizon oil spill.

Microbial communities play vital roles in the biogeochemistry of nutrients in coastal saltmarshes, ultimately controlling water quality, nutrient cycling, and detoxification. We determined the structure of microbial populations inhabiting coastal saltmarsh sediments from northern Barataria Bay, Louisiana, USA to gain insight into impacts on the biogeochemical cycles affected by Macondo oil from the 2010 Deepwater Horizon well blowout two years after the accident. Quantitative PCR directed toward specific functional genes revealed that oiled marshes were greatly diminished in the population sizes of diazotrophs, denitrifiers, nitrate-reducers to ammonia, methanogens, sulfate-reducers and anaerobic aromatic degraders, and harbored elevated numbers of alkane-degraders. Illumina 16S rRNA gene sequencing indicated that oiling greatly changed the structure of the microbial communities, including significant decreases in diversity. Oil-driven changes were also demonstrated in the structure of two functional populations, denitrifying and sulfate reducing prokaryotes, using nirS and dsrB as biomarkers, respectively. Collectively, the results from 16S rRNA and functional genes indicated that oiling not only markedly altered the microbial community structures, but also the sizes and structures of populations involved in (or regulating) a number of important nutrient biogeochemical cycles in the saltmarshes. Alterations such as these are associated with potential deterioration of ecological services, and further studies are necessary to assess the trajectory of recovery of microbial-mediated ecosystem functions over time in oiled saltmarsh sediment.

Soil seed banks and their germination responses to cadmium and salinity stresses in coastal wetlands affected by reclamation and urbanization based on indoor and outdoor experiments.

Indoor and outdoor seedling emergence experiments were conducted to thoroughly investigate germination patterns as affected by reclamation and urbanization, the ecological characteristics of soil seed banks, and their relationships with environmental factors in both urbanized and reclaimed regions of the Pearl River Delta in coastal wetlands. The germination rate of the soil seed bank was higher in the indoor experiment compared with that in the outdoor experiment, whereas the number and destiny of the germinated seedlings were greater in the outdoor experiment. The species diversity and number, as well as the richness and evenness indices, were higher in the urbanized region compared with the reclaimed region. However, the dominance and Sørensen similarity indices were greater in the reclaimed region compared with those indices in the urbanized region. Higher salinity and Cadmium (Cd) levels could inhibit seed germination; however, their suitable ranges (i.e. [0-2,000 mg kg(-1)] for salinity and [0-4.0 mg kg(-1)] for available Cd) can activate seedling emergence, and more seedlings germinated under the intersectional levels at 0.34 mg kg(-1) available Cd and 778.6 mg kg(-1) salinity. Seawater intrusion caused by the sea level rise will possibly result in the salt-tolerant community in this area due to increasing salinity.

Assessment of heavy metal pollution in wetland soils from the young and old reclaimed regions in the Pearl River Estuary, South China.

Soils were sampled in three types of wetlands from the young (A) and old (B) reclaimed regions of the Pearl River Estuary. They were analyzed for total concentrations of heavy metals to investigate their distributions and pollution levels in both regions. Results showed that most heavy metals in ditch and riparian wetlands did not significantly differ from those in reclaimed wetlands in A region, while significantly lower for Cd, Cu, Pb, and Zn in reclaimed wetlands in B region, suggesting higher effects of long-term reclamation. Iron, Cr and Cu were identified as metal pollutants of primary concern and had higher contributions to the total toxic units compared to other metals. Almost all metals exceeded their lowest effect levels and Fe and Cr even exceeded the severe effect levels. Multivariate analysis shows that Fe and Mn are controlled by parent rocks and other metals mainly originate from anthropogenic source.