Toward more sustainable tropical agriculture with cover crops: Soil microbiome responses to nitrogen management

Cover crops are a potential pathway for ecological cultivation in agricultural systems. In tropical no-till agricultural systems, the maintenance of residues on the soil surface and the addition of nitrogen (N) benefit the growth and grain yield of cash crops as well as the chemical and physical properties of the soil. However, the effects of these management practices on the soil microbiota are largely unknown. Here, we evaluated the effects of the timing of N application as a pulse disturbance and the growth of different cover crop species before maize in rotation on soil properties, maize productivity, and soil bacterial and fungal community diversity and composition. N fertilizer was applied either on live cover crops (palisade grass or ruzigrass), on cover crop straw just before maize seeding or in the maize V4 growth stage. Soils previously cultivated with palisade grass established similar microbial communities regardless of N application timing, with increases in total bacteria, total archaea, nutrients, and the C:N ratio. The soil microbial alpha diversity in treatments with palisade grass did not vary with N application timing, whereas the bacterial and fungal diversities in the treatments with ruzigrass decreased when N was applied to live ruzigrass or maize in the V4 growth stage. We conclude that palisade grass is a more suitable cover crop than ruzigrass, as palisade grass enhanced soil microbial diversity and maize productivity regardless of N application timing. Ruzigrass could be used as an alternative to palisade grass when N is applied during the straw phase. However, considering the entire agricultural system (soil–plant–microbe), ruzigrass is not as efficient as palisade grass in tropical no-till cover crop–maize rotation systems. Palisade grass is a suitable cover crop alternative for enhancing maize productivity, soil chemical properties and nutrient cycling, regardless of the timing of N application. Additionally, this study demonstrates that a holistic approach is valuable for evaluating soil diversity and crop productivity in agricultural systems

Lasting effect of Urochloa brizantha on a common bean-wheat-maize rotation in a medium-term no-till system.

Grass intercropping under no-till is an option to increase crop residues on the soil surface and crop diversity. Urochloa spp. is frequently selected for intercropping to improve land use and agricultural production because of its high residue production, slow residue decomposition, as well as its vigorous, abundant, and deep root system. However, the effects of intercropping Urochloa and maize, especially the effects of Urochloa residues, on subsequent crops in rotation have not been established. To address this knowledge gap, a field experiment was carried out over 5 years (from 2014 to 2018) comprising 2 years of maize monocropping or intercropping and 3 years of crop rotation (common bean-wheat-common bean-wheat-maize). We evaluated the medium-term effects of monocropped maize or maize intercropped with Urochloa brizantha on soil fertility and the development, yields, and grain nutrient accumulation of subsequent common bean, wheat, and maize crops. The cultivation of U. brizantha in the intercropping system improved soil fertility over at least 4 years, with increases in soil pH; soil organic matter (SOM); phosphorus (P); exchangeable potassium (K), calcium (Ca), and magnesium (Mg); sulfur (S?SO42?); cation exchange capacity (CEC); and base saturation (BS) at all soil depths. The benefits of U. brizantha extended to root dry matter and distribution; 70?77% of the total roots were concentrated within a soil depth of 0.0?0.2?m. The intercropping system improved the root dry matter mass, yield components, and grain yields of subsequent common bean, wheat, and maize crops in all cultivation years. These findings indicate that intercropping maize and U. brizantha provides medium-term benefits for subsequent common bean, wheat, and maize crops, and improves nutrient cycling to increase soil P; exchangeable K, Ca, and Mg; S?SO42?; and organic matter content

Forage Grasses Steer Soil Nitrogen Processes, Microbial Populations, and Microbiome Composition in A Long-term Tropical Agriculture System

Forage grasses used in cropping no-till systems in tropical regions alter soil chemical properties, but their long-term impact on soil microbial processes of the nitrogen (N) cycle and microbial community abundance, composition and structure are unknown. Here, microbial functions related to nitrogen fixation, nitrification and denitrification as well as bacterial, archaeal and fungal populations were evaluated in a long-term field experiment in which tropical forage grasses palisade grass (Urochloa brizantha (Hochst. Ex A. Rich.) R.D. Webster) and ruzigrass (U. ruziziensis (R. Germ. and C.M. Evrard) Crins) were cultivated with or without N fertilization. Uncultivated soil was used as a control. Forage grasses, especially palisade grass, increased soil bacterial and fungal abundances, whereas the archaeal population was highest in uncultivated soil. In soils cultivated with forage grasses, N fertilization favored N-cycle-related genes; however, cultivation of palisade grass increased the abundances of amoA bacteria (AOB) and amoA archaea (AOA) genes associated with soil nitrification and decreased the abundances of genes nirS, nirK and nosZ genes related to denitrification, compared to ruzigrass and control, regardless of N input. In addition, abundances of total bacteria and total fungi were associated with the N cycle and plant biomass in soils cultivated with forage grasses. Forage cultivation clearly benefitted the soil nutrient environment (S-SO42-, Mg2+, total-C and -N, N-NO3- and N-NH4+) and microbiome (bacteria and fungi) compared with uncultivated soil. In soil cultivated with palisade grass, the microbial community composition was unresponsive to N addition. The high N uptake by palisade grass supports the competitive advantage of this plant species over microorganisms for N sources. Our results suggest that palisade grass has advantages over ruzigrass for use in agriculture systems, regardless of N input

The role of admission surveillance cultures in patients requiring prolonged mechanical ventilation in the intensive care unit

We undertook a prospective observational cohort study in intensive care unit (ICU) patients requiring mechanical ventilation for four days or more to evaluate normal and abnormal bacterial carriage on admission detected by surveillance cultures of throat and rectum. We assessed the importance of surveillance and diagnostic cultures for the early detection of resistance to third generation cephalosporins employed as the parenteral component of the selective decontamination of the digestive tract. Finally, we sought the risk factors of abnormal carriage on admission to the ICU. During the 58-month study 621 patients were included: 186 patients (30%) carried abnormal flora including methicillin-resistant Staphylococcus aureus (MRSA) and aerobic Gram negative bacilli (AGNB) on admission to the ICU Both MRSA and AGNB carriers were more commonly present in the hospital group of patients than in patients referred from the community (P < 0.001), although overgrowth was equally present both in community and in hospital patients. The incidence of infections during ICU stay was higher in abnormal (n=120, 64.5%) than in normal carriers (n=185, 42.5%) (P < 0.0001), with an odds ratio of 2.46 (95% confidence interval 1.72 to 3.51). Third generation cephalosporins covered ICU admission flora in 482 (78%) of the studied population. AGNB resistant to cephalosporins and MRSA were detected in surveillance cultures of 139 patients (22%), while the same resistant micro-organisms were identified only in 49 diagnostic samples (7.9%). Parenteral cephalosporins were modified in patients with abnormal flora (P < 0.0001). One hundred and ninety-six patients received antibiotics before admission to the ICU and 42% carried AGNB resistant to cephalosporins. Previous antibiotic use was the only risk factor for abnormal carriage in the multivariate analysis (OR 3.5; 95% confidence interval 2.1 to 5.8). The knowledge of carriage on admission using surveillance cultures may help intensivists to identify patients with abnormal carriage on admission and resistant bacterial strains at an early stage even when diagnostic samples are negative. Third generation cephalosporins covered admission flora in about 80% of the enrolled population and were modified in patients with abnormal flora who received antibiotic therapy before ICU admission. Our finding of overgrowth present on admission may justify the immediate administration of enteral antimicrobials

Nitrogen input on organic amendments alters the pattern of soil–microbe-plant co-dependence

The challenges of nitrogen (N) management in agricultural fields include minimizing N losses while maximizing profitability and soil health. Crop residues can alter N and carbon (C) cycle processes in the soil and modulate the responses of the subsequent crop and soil– microbe-plant interactions. Here, we aim to understand how organic amendments with low and high C/N ratio, combined or not with mineral N may change soil bacterial community and their activity in the soil. Organic amendments with different C/N ratios were combined or not with N fertilization as follows: i) unamended soil (control), ii) grass clover silage (GC; low C/N ratio), and iii) wheat straw (WS; high C/N ratio). The organic amendments modulated the bacterial community assemblage and increased microbial activity. WS amendment had the strongest effects on hot water extractable carbon, microbial biomass N and soil respiration, which were linked with changes in bacterial community composition compared with GC-amended and unamended soil. By contrast, N transformation processes in the soil were more pronounced in GC-amended and unamended soil than in WS-amended soil. These responses were stronger in the presence of mineral N input. WS amendment induced greater N immobilization in the soil, even with mineral N input, impairing crop development. Interestingly, N input in unamended soil altered the co-dependence between the soil and the bacterial community to favor a new co-dependence among the soil, plant and microbial activity. In GC-amended soil, N fertilization shifted the dependence of the crop plant from the bacterial community to soil characteristics. Finally, the combined N input with WS amendment (organic carbon input) placed microbial activity at the center of the interrelationships between the bacterial community, plant, and soil. This emphasizes the crucial importance of microorganisms in the functioning of agroecosystems. To achieve higher yields in crops managed with various organic amendments, it is essential to incorporate mineral N management practices. This becomes particularly crucial when the soil amendments have a high C/N ratio

Toward more sustainable tropical agriculture with cover crops: Soil microbiome responses to nitrogen management

Cover crops are a potential pathway for ecological cultivation in agricultural systems. In tropical no-till agricultural systems, the maintenance of residues on the soil surface and the addition of nitrogen (N) benefit the growth and grain yield of cash crops as well as the chemical and physical properties of the soil. However, the effects of these management practices on the soil microbiota are largely unknown. Here, we evaluated the effects of the timing of N application as a pulse disturbance and the growth of different cover crop species before maize in rotation on soil properties, maize productivity, and soil bacterial and fungal community diversity and composition. N fertilizer was applied either on live cover crops (palisade grass or ruzigrass), on cover crop straw just before maize seeding or in the maize V4 growth stage. Soils previously cultivated with palisade grass established similar microbial communities regardless of N application timing, with increases in total bacteria, total archaea, nutrients, and the C:N ratio. The soil microbial alpha diversity in treatments with palisade grass did not vary with N application timing, whereas the bacterial and fungal diversities in the treatments with ruzigrass decreased when N was applied to live ruzigrass or maize in the V4 growth stage. We conclude that palisade grass is a more suitable cover crop than ruzigrass, as palisade grass enhanced soil microbial diversity and maize productivity regardless of N application timing. Ruzigrass could be used as an alternative to palisade grass when N is applied during the straw phase. However, considering the entire agricultural system (soil–plant–microbe), ruzigrass is not as efficient as palisade grass in tropical no-till cover crop–maize rotation systems. Palisade grass is a suitable cover crop alternative for enhancing maize productivity, soil chemical properties and nutrient cycling, regardless of the timing of N application. Additionally, this study demonstrates that a holistic approach is valuable for evaluating soil diversity and crop productivity in agricultural systems