Gallionellaceae in rice root plaque: metabolic roles in iron oxidation, nutrient cycling, and plant interactions

IMPORTANCE

In waterlogged soils, iron plaque forms a reactive barrier between the root and soil, collecting phosphate and metals such as arsenic and cadmium. It is well established that iron-reducing bacteria solubilize iron, releasing these associated elements. In contrast, microbial roles in plaque formation have not been clear. Here, we show that there is a substantial population of iron oxidizers in plaque, and furthermore, that these organisms (Sideroxydans and Gallionella) are distinguished by genes for plant colonization and nutrient fixation. Our results suggest that iron-oxidizing and iron-reducing bacteria form and remodel iron plaque, making it a dynamic system that represents both a temporary sink for elements (P, As, Cd, C, etc.) as well as a source. In contrast to abiotic iron oxidation, microbial iron oxidation results in coupled Fe-C-N cycling, as well as microbe-microbe and microbe-plant ecological interactions that need to be considered in soil biogeochemistry, ecosystem dynamics, and crop management.

A microscopic scenario on recovery mechanisms under waterlogging and submergence stress in rice

MAIN CONCLUSION

Adaptive traits in rice responding to flooding, a compound stress, are associated with morpho-anatomical and physiological changes which are regulated at the genetic level. Therefore, understanding submergence stress tolerance in rice will help development of adapted cultivars that can help mitigate agricultural losses. Rice is an important dietary component of daily human consumption and is cultivated as a staple crop worldwide. Flooding is a compound stress which imposes significant financial losses to farmers. Flood-affected rainfed rice ecosystems led to the development of various adaptive traits in different cultivars for their optimal growth and survival. Some cultivars can tolerate hypoxia by temporarily arresting elongation and conserving their energy sources, which they utilize to regrow after the stress conditions subside. However, few other cultivars rapidly elongate to escape hypoxia using carbohydrate resources. These contrasting characters are regulated at the genetic level through different quantitative trait loci that contain ERF transcription factors (TFs), Submergence and Snorkels. TFs can simultaneously activate the transcription of various genes involved in stress and development responses. These TFs are of prime importance because the introgressed and near-isogenic lines showed promising results with increased submergence tolerance without affecting yield or quality. However, the entire landscape of submergence tolerance is not entirely depicted, and further exploration in the field is necessary to understand the mechanism in rice completely. Therefore, this review will highlight the significant adaptive traits observed in flooded rice varieties and how they are regulated mechanistically.

Multiyear methane and nitrous oxide emissions in different irrigation management under long-term continuous rice rotation in Arkansas

Rice paddies are one of the major sources of anthropogenic methane (CH₄ ) emissions. The alternate wetting and drying (AWD) irrigation management has been shown to reduce CH₄ emissions and total global warming potential (GWP) (CH₄ and nitrous oxide [N₂ O]). However, there is limited information about utilizing AWD management to reduce greenhouse gas (GHG) emissions from commercial-scale continuous rice fields. This study was conducted for five consecutive growing seasons (2015-2019) on a pair of adjacent fields in a commercial farm in Arkansas under long-term continuous rice rotation irrigated with either continuously flooded (CF) or AWD conditions. The cumulative CH₄ emissions in the growing season across the two fields and 5 years ranged from 41 to 123 kg CH₄ -C ha^-1 for CF and 1 to 73 kg CH₄ -C ha^-1 for AWD. On average, AWD reduced CH₄ emissions by 73% relative to CH₄ emissions in CF fields. Compared to N₂ O emissions, CH₄ emissions dominated the GWP with an average contribution of 91% in both irrigation treatments. There was no significant variation in grain yield (7.3-11.9 Mg ha^-1 ) or growing season N₂ O emissions (-0.02 to 0.51 kg N₂ O-N ha^-1 ) between the irrigation treatments. The yield-scaled GWP was 368 and 173 kg CO₂ eq. Mg^-1 season^-1 for CF and AWD, respectively, showing the feasibility of AWD on a commercial farm to reduce the total GHG emissions while sustaining grain yield. Seasonal variations of GHG emissions observed within fields showed total GHG emissions were predominantly influenced by weather (precipitation) and crop and irrigation management. The influence of air temperature and floodwater heights on GHG emissions had high degree of variability among years and fields. These findings demonstrate that the use of multiyear GHG emission datasets could better capture variability of GHG emissions associated with rice production and could improve field verification of GHG emission models and scaling factors for commercial rice farms.

Integrated root phenotypes for improved rice performance under low nitrogen availability

Greater nitrogen efficiency would substantially reduce the economic, energy and environmental costs of rice production. We hypothesized that synergistic balancing of the costs and benefits for soil exploration among root architectural phenes is beneficial under suboptimal nitrogen availability. An enhanced implementation of the functional-structural model OpenSimRoot for rice integrated with the ORYZA_v3 crop model was used to evaluate the utility of combinations of root architectural phenes, namely nodal root angle, the proportion of smaller diameter nodal roots, nodal root number; and L-type and S-type lateral branching densities, for plant growth under low nitrogen. Multiple integrated root phenotypes were identified with greater shoot biomass under low nitrogen than the reference cultivar IR64. The superiority of these phenotypes was due to synergism among root phenes rather than the expected additive effects of phene states. Representative optimal phenotypes were predicted to have up to 80% greater grain yield with low N supply in the rainfed dry direct-seeded agroecosystem over future weather conditions, compared to IR64. These phenotypes merit consideration as root ideotypes for breeding rice cultivars with improved yield under rainfed dry direct-seeded conditions with limited nitrogen availability. The importance of phene synergism for the performance of integrated phenotypes has implications for crop breeding.

Improving Nitrogen Use Efficiency in Aerobic Rice Based on Insights Into the Ecophysiology of Archaeal and Bacterial Ammonia Oxidizers

The abundance and structural composition of nitrogen (N) transformation-related microbial communities under certain environmental conditions provide sufficient information about N cycle under different soil conditions. This study aims to explore the major challenge of low N use efficiency (NUE) and N dynamics in aerobic rice systems and reveal the agronomic-adjustive measures to increase NUE through insights into the ecophysiology of ammonia oxidizers. Water-saving practices, like alternate wetting and drying (AWD), dry direct seeded rice (DDSR), wet direct seeding, and saturated soil culture (SSC), have been evaluated in lowland rice; however, only few studies have been conducted on N dynamics in aerobic rice systems. Biological ammonia oxidation is majorly conducted by two types of microorganisms, ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). This review focuses on how diversified are ammonia oxidizers (AOA and AOB), whose factors affect their activities and abundance under different soil conditions. It summarizes findings on pathways of N cycle, rationalize recent research on ammonia oxidizers in N-cycle, and thereby suggests adjustive agronomic measures to reduce N losses. This review also suggests that variations in soil properties significantly impact the structural composition and abundance of ammonia oxidizers. Nitrification inhibitors (NIs) especially nitrapyrin, reduce the nitrification rate and inhibit the abundance of bacterial amoA without impacting archaeal amoA. In contrast, some NIs confine the hydrolysis of synthetic N and, therefore, keep low NH₄ ⁺-N concentrations that exhibit no or very slight impact on ammonia oxidizers. Variations in soil properties are more influential in the community structure and abundance of ammonia oxidizers than application of synthetic N fertilizers and NIs. Biological nitrification inhibitors (BNIs) are natural bioactive compounds released from roots of certain plant species, such as sorghum, and could be commercialized to suppress the capacity of nitrifying soil microbes. Mixed application of synthetic and organic N fertilizers enhances NUE and plant N-uptake by reducing ammonia N losses. High salt concentration promotes community abundance while limiting the diversity of AOB and vice versa for AOA, whereas AOA have lower rate for potential nitrification than AOB, and denitrification accounts for higher N₂ production. Archaeal abundance, diversity, and structural composition change along an elevation gradient and mainly depend on various soil factors, such as soil saturation, availability of NH₄ ⁺, and organic matter contents. Microbial abundance and structural analyses revealed that the structural composition of AOA was not highly responsive to changes in soil conditions or N amendment. Further studies are suggested to cultivate AOA and AOB in controlled-environment experiments to understand the mechanisms of AOA and AOB under different conditions. Together, this evaluation will better facilitate the projections and interpretations of ammonia oxidizer community structural composition with provision of a strong basis to establish robust testable hypotheses on the competitiveness between AOB and AOA. Moreover, after this evaluation, managing soils agronomically for potential utilization of metabolic functions of ammonia oxidizers would be easier.

Organic Amendments for Pathogen and Nematode Control

The loss of methyl bromide as a soil fumigant and minimal advances in the development and registration of new chemical fumigants has resulted in a resurgence of interest in the application of organic amendments (OAs) for soilborne plant pathogen and plant-parasitic nematode management. Significant progress has been made in the characterization of OAs, application of strategies for their use, and elucidation of mechanisms by which they suppress soilborne pests. Nonetheless, their utility is limited by the variability of disease control, expense, and the logistics of introducing them into crop production systems. Recent advances in molecular techniques have led to significant progress in the elucidation of the role of bacteria and fungi and their metabolic products on disease suppression with the addition of OAs. Biosolarization and anaerobic soil disinfestation, developed to manipulate systems and favor beneficial microorganisms to maximize their impact on plant pathogens, are built on a strong historical research foundation in OAs and the physical, chemical, and biological characteristics of disease-suppressive soils. This review focuses on recent applications of OAs and their potential for the management of soilborne plant pathogens and plant-parasitic nematodes, with emphasis primarily on annual fruit and vegetable production systems.

Web-based tool for calculating field-specific nutrient management for rice in India

Site-specific nutrient management (SSNM) can be an alternative to a recommendation for uniform fertilizer use across a rice (Oryza sativa L.) production system within a country or region of a country. We developed a web-based decision support tool named Nutrient Manager for Rice (NMR), which used principles of SSNM to calculate fertilizer N, P, and K rates for individual fields based on a target yield set for each field. It also used expected growth duration of the rice variety, crop establishment method, and age of transplanted seedlings to calculate days after rice establishment for each of three applications of fertilizer N. NMR enabled P rates to match estimated removal of P with harvested grain and crop residue for the target yield set for each field. We compared field-specific fertilizer recommendations from NMR with uniform application of fertilizer provided by an existing blanket fertilizer recommendation for irrigated inbred rice (BFR) and farmer's fertilizer practices (FFP) in on-farm trials conducted in 74 irrigated rice fields across three growing seasons in the Cauvery Delta, Tamil Nadu, India. Grain yield was 0.6-0.7 Mg ha^-1 higher (P ≤ 0.05) with NMR than FFP in two of the three seasons, even though total fertilizer cost was comparable or less with NMR. Yield was comparable for NMR and BFR, but NMR reduced fertilizer N and P rates and total fertilizer cost compared to BFR. Use of NMR rather than BFR also had less risk of financial loss for a farmer. The likelihood of financial loss with a switch from FFP to BFR averaged 31%. It reduced to 18% with a switch from FFP to NMR. NMR facilitated the calculation of field-specific fertilizer N, P, and K management practices, which increased fertilizer use efficiency without loss in rice yield compared to a recommended uniform fertilizer management across fields.

Projecting changes in Everglades soil biogeochemistry for carbon and other key elements, to possible 2060 climate and hydrologic scenarios

Based on previously published studies of elemental cycling in Everglades soils, we projected how soil biogeochemistry, specifically carbon, nitrogen, phosphorus, sulfur, and mercury might respond to climate change scenarios projected for 2060 by the South Florida Water Management Model. Water budgets and stage hydrographs from this model with future scenarios of a 10% increased or decreased rainfall, a 1.5 °C rise in temperature and associated increase in evapotranspiration (ET) and a 0.5 m rise in sea level were used to predict resulting effects on soil biogeochemistry. Precipitation is a much stronger driver of soil biogeochemical processes than temperature, because of links among water cover, redox conditions, and organic carbon accumulation in soils. Under the 10% reduced rainfall scenario, large portions of the Everglades will experience dry down, organic soil oxidation, and shifts in soil redox that may dramatically alter biogeochemical processes. Lowering organic soil surface elevation may make portions of the Everglades more vulnerable to sea level rise. The 10% increased rainfall scenario, while potentially increasing phosphorus, sulfur, and mercury loading to the ecosystem, would maintain organic soil integrity and redox conditions conducive to normal wetland biogeochemical element cycling. Effects of increased ET will be similar to those of decreased precipitation. Temperature increases would have the effect of increasing microbial processes driving biogeochemical element cycling, but the effect would be much less than that of precipitation. The combined effects of decreased rainfall and increased ET suggest catastrophic losses in carbon- and organic-associated elements throughout the peat-based Everglades.