Microbial Community Functional Potential and Composition Are Shaped by Hydrologic Connectivity in Riverine Floodplain Soils

Response of bacterial communities and soil chemistry to flood durations and recovery phases

Flooding profoundly impacts soil bacterial communities; however, the underlying mechanisms remain poorly understood. This study investigated how flooding (3, 8, and 16 days) and post-flooding (immediately and 2, 5, and 30 days) durations affect soil physicochemical properties, bacterial communities, and their interactions-crucial factors in floodplain nutrient and carbon cycling. The results showed that bacteria constituted 99.9% of the total microbial composition, while archaea, contributing only 0.1%, had a negligible impact on soil traits. At 2-5 days after flooding (DAF), elevated soil electrical conductivity (EC) and pH enhanced soil bacterial abundance and activity, leading to increased water-extractable dissolved organic carbon (DOC), water-extractable total dissolved nitrogen, and biological production (BIX), accompanied by the degradation of soil organic matter (SOM) and aromatic compounds (SUVA254). These changes indicated robust interactions between soil bacterial communities and physicochemical properties affected by flooding events. However, these relationships weakened at 30 DAF, suggesting potential transitions from anaerobic to aerobic conditions in post-flooding soils after 5 DAF. Structural equation modelling indicated that an extended post-flooding duration increased BIX, accompanied by SOM and DOC degradation, providing nutrients and energy to soil microbes and consequently leading to increased bacterial diversity. This study underscores the significant impact of flooding and post-flooding durations on soil bacterial community composition and diversity, mediated by changes in EC, pH, SOM, and DOM, potentially influencing nutrient cycling in floodplains.

Do restoration strategies in mangroves recover microbial diversity? A case study in the Yucatan peninsula

Mangrove forests are fundamental coastal ecosystems for the variety of services they provide, including green-house gas regulation, coastal protection and home to a great biodiversity. Mexico is the fourth country with the largest extension of mangroves of which 60% occurs in the Yucatan Peninsula. Understanding the microbial component of mangrove forests is necessary for their critical roles in biogeochemical cycles, ecosystem health, function and restoration initiatives. Here we study the relation between the microbial community from sediments and the restoration process of mangrove forests, comparing conserved, degraded and restored mangroves along the northern coast of the Yucatan peninsula. Results showed that although each sampling site had a differentiated microbial composition, the taxa belonged predominantly to Proteobacteria (13.2-23.6%), Desulfobacterota (7.6-8.3%) and Chloroflexi (9-15.7%) phyla, and these were similar between rainy and dry seasons. Conserved mangroves showed significantly higher diversity than degraded ones, and restored mangroves recovered their microbial diversity from the degraded state (Dunn test p-value Benjamini-Hochberg adjusted = 0.0034 and 0.0071 respectively). The structure of sediment microbial β-diversity responded significantly to the mangrove conservation status and physicochemical parameters (organic carbon content, redox potential, and salinity). Taxa within Chloroflexota, Desulfobacterota and Thermoplasmatota showed significantly higher abundance in degraded mangrove samples compared to conserved ones. This study can help set a baseline that includes the microbial component in health assessment and restoration strategies of mangrove forests.

Tracing the pathways by which flood duration impacts soil bacteria through soil properties and water-extractable dissolved organic matter: A soil column experiment

Soil microbial communities control biogeochemical processes, nutrient cycling, and organic carbon storage and release in wetlands, which are influenced by flooding. To predict soil nutrient function in wetland ecosystems, understanding the effect of flooding on soil biogeochemical cycling and energy flux, including soil properties, dissolved organic matter (DOM), and microbial communities is essential. This study investigated how different flood durations (1, 3, 8, 16, and 30 d) affect the interactions between physicochemical properties and bacterial communities in a river wetland. The DOM composition was measured using ultraviolet/visible spectrophotometry coupled with fluorescence spectroscopy, and the bacterial communities were identified using 16S rRNA sequencing. Simpson's diversity index varied from 0.92 to 0.94, indicating high bacterial diversity throughout the treatments; the highest and lowest bacterial diversities were found at 1 and 8 flooding days, respectively. The abundance of Desulturomonadales, Clostridiales, Bacteroidales, and Gaiellales was positively correlated with pH, electrical conductivity, water-extractable dissolved organic carbon (WEOC), and water-extractable total dissolved nitrogen (TDN) but negatively correlated with dissolved oxygen (DO) and soil organic matter (SOM), suggesting complex interactions among these factors in response to flooding. Structural equation model revealed that flooding directly increased TDN but indirectly increased WEOC through increasing soil pH; and directly decreased DO and SOM, leading to decreases in total protein-like fraction. Three significant pathways were identified, showing the impacts of flooding on bacterial diversity: (1) flood duration decreased DO, resulting in decreased bacterial diversity; (2) flood duration decreased SOM, leading to increased bacterial diversity; and (3) flood duration decreased DO and SOM, leading to increased bacterial diversity via decreased total protein-like fraction. This study indicated that prolonged flooding has both positive and negative impacts on bacterial diversity, depending on environmental factors. It highlights the importance of flooding in shaping soil bacterial communities, with implications for nutrient cycling and carbon storage in wetlands.

Deterministic factors modulating assembly of groundwater microbial community in a nitrogen-contaminated and hydraulically-connected river-lake-floodplain ecosystem

The river-lake-floodplain system (RLFS) undergoes intensive surface-groundwater mass and energy exchanges. Some freshwater lakes are groundwater flow-through systems, serving as sinks for nitrogen (N) entering the lake. Despite the threat of cross-nitrogen contamination, the assembly of the microbial communities in the RLFS was poorly understood. Herein, the distribution, co-occurrence, and assembly pattern of microbial community were investigated in a nitrogen-contaminated and hydraulically-connected RLFS. The results showed that nitrate was widely distributed with greater accumulation on the south than on the north side, and ammonia was accumulated in the groundwater discharge area (estuary and lakeshore). The heterotrophic nitrifying bacteria and aerobic denitrifying bacteria were distributed across the entire area. In estuary and lakeshore with low levels of oxidation-reduction potential (ORP) and high levels of total organic carbon (TOC) and ammonia, dissimilatory nitrate reduction to ammonium (DNRA) bacteria were enriched. The bacterial community had close cooperative relationships, and keystone taxa harbored nitrate reduction potentials. Combined with multivariable statistics and self-organizing map (SOM) results, ammonia, TOC, and ORP acted as drivers in the spatial evolution of the bacterial community, coincidence with the predominant deterministic processes and unique niche breadth for microbial assembly. This study provides novel insight into the traits and assembly of bacterial communities and potential nitrogen cycling capacities in RLFS groundwater.

Is a floodplain forest a valuable source for lignin-degrading anaerobic microbial communities: A metagenomic approach

Lignin is one of the most substantial obstacles in the evaluation of lignocellulosic compounds. Although there are numerous approaches for the enhancement of lignin digestion in the literature, there has yet to be an optimized system to date. In this study, samples taken from Igneada floodplain forests were enriched anaerobically at 25 °C and 37 °C, with alkali lignin as the sole carbon source. The activity of the anaerobic lignin-degrading microbial consortium was detected more efficiently at 37 °C, where biogas production exceeded 3.5 mLgas/mLmedium. It was observed that the microbial community initially dominated by Proteobacteria (around 60%) changed completely after enrichment and was led by members of the Firmicutes phylum (up to 90%). The dominant species (Sporomusa termitida, Desulfitobacterium hafniense, Citrobacter freundii, Citrobacter portucalensis, Alkalibacter rhizosphaerae, and Gudongella oleilytica) occupying more than 50% in the final enrichment culture were only around 2% in the raw samples. Therefore, this study, one of the few in which enriched environmental samples were sequenced using MinION, demonstrated that longoses are exceptional reservoirs for lignin-digesting anaerobic microorganisms.

Mill dams impact microbiome structure and depth distribution in riparian sediments

Introduction

Damming has substantially fragmented and altered riverine ecosystems worldwide. Dams slow down streamflows, raise stream and groundwater levels, create anoxic or hypoxic hyporheic and riparian environments and result in deposition of fine sediments above dams. These sediments represent a good opportunity to study human legacies altering soil environments, for which we lack knowledge on microbial structure, depth distribution, and ecological function.

Methods

Here, we compared high throughput sequencing of bacterial/ archaeal and fungal community structure (diversity and composition) and functional genes (i.e., nitrification and denitrification) at different depths (ranging from 0 to 4 m) in riparian sediments above breached and existing milldams in the Mid-Atlantic United States.

Results

We found significant location- and depth-dependent changes in microbial community structure. Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, Chloroflexi, Acidobacteria, Planctomycetes, Thaumarchaeota, and Verrucomicrobia were the major prokaryotic components while Ascomycota, Basidiomycota, Chytridiomycota, Mortierellomycota, Mucoromycota, and Rozellomycota dominated fungal sequences retrieved from sediment samples. Ammonia oxidizing genes (amoA for AOA) were higher at the sediment surface but decreased sharply with depth. Besides top layers, denitrifying genes (nosZ) were also present at depth, indicating a higher denitrification potential in the deeper layers. However, these results contrasted with in situ denitrification enzyme assay (DEA) measurements, suggesting the presence of dormant microbes and/or other nitrogen processes in deep sediments that compete with denitrification. In addition to enhanced depth stratification, our results also highlighted that dam removal increased species richness, microbial diversity, and nitrification.

Discussion

Lateral and vertical spatial distributions of soil microbiomes (both prokaryotes and fungi) suggest that not only sediment stratification but also concurrent watershed conditions are important in explaining the depth profiles of microbial communities and functional genes in dammed rivers. The results also provide valuable information and guidance to stakeholders and restoration projects.

Microbially mediated Fe-N coupled cycling at different hydrological regimes in riparian wetland

Although the significance of the coupled Fe- and N- cycling processes on biogeochemical transformation in riparian wetlands is well-known, the regulation associated with the changes on the microbiotas during different hydrological regimes remains unclear. This study performed field investigations on the bacterial community compositions (BCC) and specific genera associated to Fe- and N- cycling in the rhizosphere soil and sediments in a riparian wetland in Poyang lake, China. The predominant phyla Proteobacteria, Acidobacteria, and Nitrospirae from all the samples remarkably decreased after long-term continuous flooding, while Actinobacteria, Firmicutes and Bacteroidetes were enriched. For the family level, the relative abundances of iron-oxidizing bacteria (FeOB) Gallionellaceae, and N fixing bacteria Nitrospiraceae and Bradyrhizobiaceae significantly declined upon the long-term flooding and then increased with dewatering, which were consistent with the functional genes sequencing analysis. In which, the Bradyrhizobiaceae (RA 2.0 %-34.6 %) was the dominant nirS denitrifier and potential iron-reducing bacteria (FeRB), Sideroxydans lithotrophicus was one of the dominant FeOB (RA 1.7 %-23 %), which was also identified to be the nirS dentrifier (RA 0.2 %-4.3 %). The absolute quantification of the functional genes levels including nirS, nirK, FeRB (Geobacter spp.) showed their significant increases by 3-7 times upon desiccation compared to that under post-CF. The PCA and RDA results indicated the linkage between redox changes of N and Fe during inundation mediated by FeRB, NOB, and FeOB, which were closely related to hydrochemical indices NO₃^-, Fe²⁺ and SO₄^2-. These evidences all implied the likely occurrence of nitrate reduction coupled to Fe(II) oxidation (NRFeOx) under oligotrophic conditions, which was potentially facilitated by metabolizers consisting of highly correlated Bradyrhizobiaceae and Sideroxydans (rho = 0.86, p < 0.01). These findings provide an interpretation of the biological reactions in the microbially mediated NRFeOx processes driven by hydrological change, which could assist the mechanistic understanding of the global biogeochemical cycles of iron and nitrogen in riparian wetlands.

Effects of rice-prawn (Macrobrachium nipponense) co-culture on the microbial community of soil

In the Lixiahe region of China, co-culture has been rapidly promoted in flooded paddy fields owing to its ecological and economic benefits. Rice-prawn co-culture can reduce the damage of crab and shrimp to rice growth and paddy field and substantially change the soil microbial community and soil fertility. In this study, we compared changes in the soil microbial community and soil fertility in waterlogged paddies under conventional rice culture (CR), rice-prawn (Macrobrachium nipponense) co-culture (RP), and pond culture (PC). The microbial abundance in RP was significantly higher than that in CR. RP soil microbial diversity was significantly higher than PC soil microbial diversity. The dominant bacteria in RP soil were Proteobacteria, Chloroflexi, and Bacteroidetes. Compared with those in CR, total organic matter (TOM) and total nitrogen in RP were relatively stable, available potassium and available phosphorus (AP) decreased, and other indicators increased significantly. Soil fertility significantly benefited from co-culture, with total organic carbon (TOC) increasing. Interactive relationship analysis showed that TOM, TOC, AP, and NH₄⁺-N were the main factors affecting the microbial community. Co-occurrence network analyses showed that network modularity increased with co-culture, indicating that a unique soil microbial community formed under co-culture, improving the adaptability and tolerance to co-culture. Thus, RP is a suitable culture method for this commercially important species. The results of this study can inform the practical operation of fertilizer use and sustainable development of rice-prawn aquaculture systems. KEY POINTS: • Microbial abundance and diversity increased under rice-prawn co-culture. • Co-culture significantly improved soil fertility, with an increase in TOC. • Rice-prawn co-culture is an ecologically suitable culture method for prawns.

Hydrological connectivity promotes coalescence of bacterial communities in a floodplain

Floodplains play essential roles in the ecological functions of regional environments. The merging and coalescence of bacterial communities in aquatic environments results in periodic patterns driven by regular hydrological activities, which may, in turn, influence ecological activities. However, the degree of bacterial community coalescence in the lateral and vertical directions as well as the underlying hydrological mechanism of floodplain ecosystems is poorly understood. Therefore, we investigated the spatiotemporal patterns and coalescence processes of planktonic and sedimentary bacterial communities during normal and high-water periods in a floodplain ecosystem of the Yellow River source region. We classified bacterial operational taxonomic units (OTUs) based on 16S rRNA gene sequencing, and quantified community coalescence by calculating the proportions of overlapping OTUs, the contributions of upstream sources to downstream sinks, and positive/negative cohesion. The results revealed major differences in the composition and diversity of planktonic and sedimentary bacterial communities. Bacterial community diversity in the high-water period was higher than in the normal period. Laterally, hydrological connectivity promoted the immigration and coalescence of bacterial communities to oxbow lakes in both the mainstream and tributaries, with the coalescence degree of planktonic bacteria (2.9%) higher than that of sedimentary bacteria (1.7%). Vertically, the coalescence degree of mainstream planktonic and sedimentary bacterial communities was highest, reaching 2.9%. Co-occurrence network analysis revealed that hydrological connectivity increased the complexity of the bacterial network and enhanced the coalescence of keystone species to oxbow lakes. Furthermore, community coalescence improved the competitiveness and dispersal of bacterial communities. This study demonstrated that coalescence of bacterial communities is driven by hydrological connectivity in a floodplain ecosystem. Further studies should investigate the processes of bacterial community coalescence in floodplains in more detail, which could provide new approaches for environmental protection and ecological function preservation.

Levees don't protect, they disconnect: A critical review of how artificial levees impact floodplain functions

Despite the recognition of floodplain importance in the scientific community, floodplains are not afforded the same legal protection as river channels. In the United States alone, flood-related economic losses were much higher in the second half of the 20th century than the first half despite the expenditure of billions of dollars on flood defenses. Partially to blame are the low appraisal and understanding of human impacts to floodplain functions. Here, we explore the impacts of levees on floodplain functions and analyze case studies of floodplain restoration through levee removal. Floodplain functions include (1) fluxes of water, solutes, and particulate materials; (2) enhanced spatial heterogeneity of hydrology and biogeochemistry; (3) enhanced habitat abundance and diversity; (4) enhanced biomass and biodiversity; and (5) hazard mitigation. Case studies of floodplain restoration involving artificial levee adjustment are heavily concentrated in North America, Europe, and Japan, and those case studies assess floodplain functions within 30 years of restoration. In the United States, restoration through levee removal comprises less than 1% of artificial levee length and 1-2% of disconnected floodplains. In Europe, restoration effectiveness was severely limited by upstream flow regulation. Most case studies were impacted by stressors outside the study site and took place in lowland alluvial rivers. Reconfiguration was successful at achieving limited aims while reconnection set floodplains on a trajectory to more fully restore floodplain functions. Case studies illustrated the tension between restoration scale and study resolution in time and space as well as the role of site-specific characteristics in determining restoration outcomes. Numerous knowledge gaps surrounding the integrative relationships between floodplain functions must be addressed in future studies. The ubiquity of flow regulation demands that future floodplain restoration occur in a whole-of-basin manner. Monitoring of restoration must take place for longer periods of time and include multiple functions.

Assessment of Fusarium-Damaged Kernels in Common Wheat in Romania in the Years 2015 and 2016 with Extreme Weather Events

This article assesses the occurrence of Fusarium-damaged kernels (FDKs) in common wheat (Triticum aestivum) under the influence of environmental factors and extreme weather events in Romania (exceptionally high air temperatures and extreme pedological drought produced by a dipole block in summer 2015, and extreme precipitation and floods produced by an omega block in spring 2016). Wheat samples (N = 272) were analyzed for FDKs via visual estimation and manual weighing according to ISO 7970 and are statistically evaluated using SPSS. The dipole block in 2015 reduced the effects of environmental factors to non-significant correlations with FDKs, while the omega block in 2016 was non-significantly to very significantly correlated with FDKs in the northwestern and western regions. The occurrence of FDKs was favored for wheat cultivation in acidic soils and inhibited in alkaline soils. Wheat samples with FDKs ≥ 1% were sampled from crops grown in river meadows with high and very high risks of flooding. Knowing the contaminants' geographical and spatial distributions under the influence of regular and extreme weather events is important for establishing measures to mitigate the effects of climate change and to ensure human and animal health.

Can Model Experiments Give Insight into the Response of the Soil Environment to Flooding? A Comparison of Microcosm and Natural Event

Studies using soil microcosms are very common, but few involve flooded soils, and comparing the results from such an experiment with natural conditions is unheard of. In the present study, we investigated the biological activity of soil (pH value, dehydrogenases and phosphatase activities) and the metabolic potential (EcoPlate™ Biolog®) of soil microorganisms in three fluvisol subjected to flooding under laboratory and natural conditions. The results indicate that soil flooding under both natural and laboratory conditions affected soil pH, enzymatic activity and metabolic potential (AWCD, average well colour development) of soil microorganisms. Changes in these parameters are more pronounced in the microcosmic experiment than in the field conditions. Furthermore, depending on the characteristics of the soil (i.e., its type, structure, vegetation) some of the soil quality parameters may return to their preflood state. Microcosm studies are needed in environmental ecology and microbiology to predict changes due to various factors, but their scale and course must be carefully planned.

Flooding Causes Dramatic Compositional Shifts and Depletion of Putative Beneficial Bacteria on the Spring Wheat Microbiota

Flooding affects both above- and below-ground ecosystem processes, and it represents a substantial threat for crop and cereal productivity under climate change. Plant-associated microbiota play a crucial role in plant growth and fitness, but we still have a limited understanding of the response of the crop-microbiota complex under extreme weather events, such as flooding. Soil microbes are highly sensitive to abiotic disturbance, and shifts in microbial community composition, structure and functions are expected when soil conditions are altered due to flooding events (e.g., anoxia, pH alteration, changes in nutrient concentration). Here, we established a pot experiment to determine the effects of flooding stress on the spring wheat-microbiota complex. Since plant phenology could be an important factor in the response to hydrological stress, flooding was induced only once and at different plant growth stages (PGSs), such as tillering, booting and flowering. After each flooding event, we measured in the control and flooded pots several edaphic and plant properties and characterized the bacterial community associated to the rhizosphere and roots of wheat plant using a metabarcoding approach. In our study, flooding caused a significant reduction in plant development and we observed dramatic shifts in bacterial community composition at each PGS in which the hydrological stress was induced. However, a more pronounced disruption in community assembly was always shown in younger plants. Generally, flooding caused a (i) significant increase of bacterial taxa with anaerobic respiratory capabilities, such as members of Firmicutes and Desulfobacterota, (ii) a significant reduction in Actinobacteria and Proteobacteria, (iii) depletion of several putative plant-beneficial taxa, and (iv) increases of the abundance of potential detrimental bacteria. These significant differences in community composition between flooded and control samples were correlated with changes in soil conditions and plant properties caused by the hydrological stress, with pH and total N as the soil, and S, Na, Mn, and Ca concentrations as the root properties most influencing microbial assemblage in the wheat mircobiota under flooding stress. Collectively, our findings demonstrated the role of flooding on restructuring the spring wheat microbiota, and highlighted the detrimental effect of this hydrological stress on plant fitness and performance.

Microbial communities in floodplain ecosystems in relation to altered flow regimes and experimental flooding

River floodplains are spatially diverse ecosystems that respond quickly to flow variations and disturbance. However, it remains unclear how flow alteration and hydrological disturbance impacts the structure and biodiversity of complex microbial communities in these ecosystems. Here, we examined the spatial and seasonal dynamics of microbial communities in aquatic (benthic) and terrestrial habitats of three hydrologically contrasting (natural flow, residual flow, hydropeaking flow) floodplain systems. Microbial communities (alpha and beta diversity) differed more among floodplain habitats than between riverine floodplains. Microbial communities in all systems displayed congruent seasonal effects. In the residual and hydropeaking systems, an experimental flood was released from a reservoir to mimic a natural high flow event causing hydromorphological disturbance. The experimental flood caused a temporary shift in microbial communities by releasing microbes from the reservoir as well as redistributing communities among floodplain habitats. The flood-mediated shift in community structures had only a transient impact as pelagic bacteria did not persist within floodplain habitats over time after the flood. More frequent pulse disturbances might lead to an alternate structure of bacterial communities in floodplains over time.

Deoxynivalenol Occurrence in Triticale Crops in Romania during the 2012-2014 Period with Extreme Weather Events

This article aims to evaluate deoxynivalenol occurrence in triticale crops in Romania in years with extreme weather events (2012: Siberian anticyclone with cold waves and heavy snowfall; 2013 and 2014: “Vb” cyclones with heavy precipitation and floods in spring). The deoxynivalenol level in triticale samples (N = 236) was quantified by ELISA. In Romania, the extreme weather events favoured deoxynivalenol occurrence in triticale in Transylvania and the Southern Hilly Area (44–47° N, 22–25° E) with a humid/balanced-humid temperate continental climate, luvisols and high/very high risk of floods. Maximum deoxynivalenol contamination was lower in the other regions, although heavy precipitation in May–July 2014 was higher, with chernozems having higher aridity. Multivariate analysis of the factors influencing deoxynivalenol occurrence in triticale showed at least a significant correlation for all components of variation source (agricultural year, agricultural region, average of deoxynivalenol, average air temperature, cumulative precipitation, soil moisture reserve, aridity indices) (p-value < 0.05). The spatial and geographic distribution of deoxynivalenol in cereals in the countries affected by the 2012–2014 extreme weather events revealed a higher contamination in Central Europe compared to southeastern and eastern Europe. Deoxynivalenol occurrence in cereals was favoured by local and regional agroclimatic factors and was amplified by extreme weather events.

Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale

BACKGROUND

Biogeochemical exports from watersheds are modulated by the activity of microorganisms that function over micron scales. Here, we tested the hypothesis that meander-bound regions share a core microbiome and exhibit patterns of metabolic potential that broadly predict biogeochemical processes in floodplain soils along a river corridor.

RESULTS

We intensively sampled the microbiomes of floodplain soils located in the upper, middle, and lower reaches of the East River, Colorado. Despite the very high microbial diversity and complexity of the soils, we reconstructed 248 quality draft genomes representative of subspecies. Approximately one third of these bacterial subspecies was detected across all three locations at similar abundance levels, and ~ 15% of species were detected in two consecutive years. Within the meander-bound floodplains, we did not detect systematic patterns of gene abundance based on sampling position relative to the river. However, across meanders, we identified a core floodplain microbiome that is enriched in capacities for aerobic respiration, aerobic CO oxidation, and thiosulfate oxidation with the formation of elemental sulfur. Given this, we conducted a transcriptomic analysis of the middle floodplain. In contrast to predictions made based on the prominence of gene inventories, the most highly transcribed genes were relatively rare amoCAB and nxrAB (for nitrification) genes, followed by genes involved in methanol and formate oxidation, and nitrogen and CO₂ fixation. Within all three meanders, low soil organic carbon correlated with high activity of genes involved in methanol, formate, sulfide, hydrogen, and ammonia oxidation, nitrite oxidoreduction, and nitrate and nitrite reduction. Overall, the results emphasize the importance of sulfur, one-carbon and nitrogen compound metabolism in soils of the riparian corridor.

CONCLUSIONS

The disparity between the scale of a microbial cell and the scale of a watershed currently limits the development of genomically informed predictive models describing watershed biogeochemical function. Meander-bound floodplains appear to serve as scaling motifs that predict aggregate capacities for biogeochemical transformations, providing a foundation for incorporating riparian soil microbiomes in watershed models. Widely represented genetic capacities did not predict in situ activity at one time point, but rather they define a reservoir of biogeochemical potential available as conditions change. Video abstract.

Flooding variations affect soil bacterial communities at the spatial and inter-annual scales

Hydrological variations have substantial effects on the diversity and composition of soil bacterial communities in wetlands. At the spatial scale, the responses of soil bacterial diversity and composition to hydrological variations in wetlands have been extensively investigated. However, at the temporal scale, especially at the inter-annual scale, the corresponding bacterial responses are rarely reported. Therefore, we explored the effects of flooding variations on the diversity and composition of soil bacterial communities at a lakeshore wetland in two hydrological contrasting years. Three flooding variables, i.e. flooding duration (FD), total duration of the growing season (TGD), and exposure duration of the growing season (EGD), were used to characterize flooding regime. Soil bacterial communities were determined using 16S rRNA gene sequencing method. We found a very high soil bacterial diversity at the lakeshore wetland. The Shannon's indexes of soil bacterial communities varied from 5.61 to 7.11 in two years. Soil bacterial α-diversity followed a unimodal curve along the elevation gradient, and was significantly lower in the flooding year than in the drought year. Principal coordinate analysis demonstrated that the compositions of soil bacterial communities were separated in order of elevation and year along the first and second axes, respectively. The apparent habitat preferences of soil bacterial families were closely connected with their respiratory traits, and this trend was stronger at the inter-annual scale than at the spatial scale. Soil bacterial compositions were predominantly determined by the direct (by changing respiratory traits) and indirect (by changing soil pH) effects of TGD at the spatial scale, while they were simultaneously regulated by the direct effects of three flooding variables at the inter-annual scale. Our results enhance the understanding of soil microbial communities in wetlands and have large implications for developing general theories to predicting soil microbial functions.

Floodplain soil and its bacterial composition are strongly affected by depth

We studied bacterial abundance and community structure of five soil cores using high-throughput sequencing of the 16S rRNA gene. Shifts in the soil bacterial composition were more pronounced within a vertical profile than across the landscape. Soil organic carbon (SOC) and nitrogen (N) concentrations decreased exponentially with soil depth and revealed a buried carbon-rich horizon between 0.8 and 1.3 m across all soil cores. This buried horizon was phylogenetically similar to its surrounding subsoils supporting the idea that the type of carbon, not necessarily the amount of carbon was driving the apparent similarities. In contrast to other studies, Nitrospirae was one of our major phyla with relatively high abundances throughout the soil profile except for the surface soil. Although depth is the major driver shaping soil bacterial community structure, positive correlations with SOC and N concentrations, however, were revealed with the bacterial abundance of Acidobacteria, one of the major, and Gemmatimonadetes, one of the minor phyla in our study. Our study showed that bacterial diversity in soils below 2.0 m can be still as high if not higher than in the above laying subsurface soil suggesting that various bacteria throughout the soil profile influence major biogeochemical processes in floodplain soils.

Functional Analysis of a Polluted River Microbiome Reveals a Metabolic Potential for Bioremediation

The objective of this study is to understand the functional and metabolic potential of the microbial communities along the Apatlaco River and highlight activities related to bioremediation and its relationship with the Apatlaco’s pollutants, to enhance future design of more accurate bioremediation processes. Water samples were collected at four sampling sites along the Apatlaco River (S1–S4) and a whole metagenome shotgun sequencing was performed to survey and understand the microbial metabolic functions with potential for bioremediation. A HMMER search was used to detect sequence homologs related to polyethylene terephthalate (PET) and polystyrene biodegradation, along with bacterial metal tolerance in Apatlaco River metagenomes. Our results suggest that pollution is a selective pressure which enriches microorganisms at polluted sites, displaying metabolic capacities to tolerate and transform the contamination. According to KEGG annotation, all sites along the river have bacteria with genes related to xenobiotic biodegradation. In particular, functions such as environmental processing, xenobiotic biodegradation and glycan biosynthesis are over-represented in polluted samples, in comparison to those in the clean water site. This suggests a functional specialization in the communities that inhabit each perturbated point. Our results can contribute to the determination of the partition in a metabolic niche among different Apatlaco River prokaryotic communities, that help to contend with and understand the effect of anthropogenic contamination.

Measuring soil sustainability via soil resilience

Soils are the nexus of water, energy and food, which illustrates the need for a holistic approach in sustainable soil management. The present study therefore aimed at identifying a bioindicator for the evaluation of soil management sustainability in a cross-disciplinary approach between soil science and multi-omics research. For this purpose we first discuss the remaining problems and challenges of evaluating sustainability and consequently suggest one measurable bioindicator for soil management sustainability. In this concept, we define soil sustainability as the maintenance of soil functional integrity. The potential to recover functional and structural integrity after a disturbance is generally defined as resilience. This potential is a product of the past and the present soil management, and at the same time prospect of possible soil responses to future disturbances. Additionally, it is correlated with the multiple soil functions and hence reflecting the multifunctionality of the soil system. Consequently, resilience can serve as a bioindicator for soil sustainability. The measurable part of soil resilience is the response diversity, calculated from the systematic contrasting of multi-omic markers for genetic potential and functional activity, and referred to as potential Maximum Ecological Performance (MEPpot) in this study. Calculating MEPpot will allow to determine the thresholds of resistance and resilience and potential tipping points for a regime shift towards irreversible or permanent unfavorable soil states for each individual soil considered. The calculation of such ecosystem thresholds is to our opinion the current global cross-disciplinary challenge.

Increased Denitrification Rates Associated with Shifts in Prokaryotic Community Composition Caused by Varying Hydrologic Connectivity

While modern developments in agriculture have allowed for increases in crop yields and rapid human population growth, they have also drastically altered biogeochemical cycles, including the biotransformation of nitrogen. Denitrification is a critical process performed by bacteria and fungi that removes nitrate in surface waters, thereby serving as a potential natural remediation strategy. We previously reported that constant inundation resulted in a coupling of denitrification gene abundances with denitrification rates in sediments, but these relationships were not maintained in periodically-inundated or non-inundated environments. In this study, we utilized Illumina next-generation sequencing to further evaluate how the microbial community responds to these hydrologic regimes and how this community is related to denitrification rates at three sites along a creek in an agricultural watershed over 2 years. The hydrologic connectivity of the sampling location had a significantly greater influence on the denitrification rate (P = 0.010), denitrification gene abundances (P < 0.001), and the prokaryotic community (P < 0.001), than did other spatiotemporal factors (e.g., creek sample site or sample month) within the same year. However, annual variability among denitrification rates was also observed (P < 0.001). Furthermore, the denitrification rate was significantly positively correlated with water nitrate concentration (Spearman's ρ = 0.56, P < 0.0001), denitrification gene abundances (ρ = 0.23-0.47, P ≤ 0.006), and the abundances of members of the families Burkholderiaceae, Anaerolinaceae, Microbacteriaceae, Acidimicrobineae incertae sedis, Cytophagaceae, and Hyphomicrobiaceae (ρ = 0.17-0.25, P ≤ 0.041). Prokaryotic community composition accounted for the least amount of variation in denitrification rates (22%), while the collective influence of spatiotemporal factors and gene abundances accounted for 37%, with 40% of the variation related to interactions among all parameters. Results of this study suggest that the hydrologic connectivity at each location had a greater effect on the prokaryotic community than did spatiotemporal differences, where inundation is associated with shifts favoring increased denitrification potential. We further establish that while complex interactions among the prokaryotic community influence denitrification, the link between hydrologic connectivity, microbial community composition, and genetic potential for biogeochemical cycling is a promising avenue to explore hydrologic remediation strategies such as periodic flooding.