Impact of diversified cropping systems and fertilization strategies on soil microbial abundance and functional potentials for nitrogen cycling

Diversified cropping systems and fertilization strategies were proposed to enhance the abundance and diversity of the soil microbiome, thereby stabilizing their beneficial services for maintaining soil fertility and supporting plant growth. Here, we assessed across three different long-term field experiments in Europe (Netherlands, Belgium, Northern Germany) whether diversified cropping systems and fertilization strategies also affect their functional gene abundance. Soil DNA was analyzed by quantitative PCR for quantifying bacteria, archaea and fungi as well as functional genes related to nitrogen (N) transformations; including bacterial and archaeal nitrification (amoA-bac,arch), three steps of the denitrification process (nirK, nirS and nosZ-cladeI,II) and N2 assimilation (nifH), respectively. Crop diversification and fertilization strategies generally enhanced soil total carbon (C), N and microbial abundance, but with variation between sites. Overall effects of diversified cropping systems and fertilization strategies on functional genes were much stronger than on the abundance of bacteria, archaea and fungi. The legume-based cropping systems showed great potential not only in stimulating the growth of N-fixing microorganisms but also in boosting downstream functional potentials for N cycling. The sorghum-based intercropping system suppressed soil ammonia oxidizing prokaryotes. N fertilization reduced the abundance of nitrifiers and denitrifiers except for ammonia-oxidizing bacteria, while the application of the synthetic nitrification inhibitor DMPP combined with mineral N reduced growth of both ammonia-oxidizing bacteria and archaea. In conclusion, this study demonstrates a strong impact of diversified agricultural practices on the soil microbiome and their functional potentials mediating N transformations.

Phylogenomic analysis reveals five independently evolved African forage grass clades in the genus Urochloa

BACKGROUND AND AIMS

The grass genus Urochloa (Brachiaria) sensu lato includes forage crops that are important for beef and dairy industries in tropical and sub-tropical Africa, South America and Oceania/Australia. Economically important species include U. brizantha, U. decumbens, U. humidicola, U. mutica, U. arrecta, U. trichopus, U. mosambicensis and Megathyrsus maximus, all native to the African continent. Perennial growth habits, large, fast growing palatable leaves, intra- and interspecific morphological variability, apomictic reproductive systems and frequent polyploidy are widely shared within the genus. The combination of these traits probably favoured the selection for forage domestication and weediness, but trait emergence across Urochloa cannot be modelled, as a robust phylogenetic assessment of the genus has not been conducted. We aim to produce a phylogeny for Urochloa that includes all important forage species, and identify their closest wild relatives (crop wild relatives). Finally, we will use our phylogeny and available trait data to infer the ancestral states of important forage traits across Urochloa s.l. and model the evolution of forage syndromes across the genus.

METHODS

Using a target enrichment sequencing approach (Angiosperm 353), we inferred a species-level phylogeny for Urochloa s.l., encompassing 54 species (~40 % of the genus) and outgroups. Phylogenies were inferred using a multispecies coalescent model and maximum likelihood method. We determined the phylogenetic placement of agriculturally important species and identified their closest wild relatives, or crop wild relatives, based on well-supported monophyly. Further, we mapped key traits associated with Urochloa forage crops to the species tree and estimated ancestral states for forage traits along branch lengths for continuous traits and at ancestral nodes in discrete traits.

KEY RESULTS

Agricultural species belong to five independent clades, including U. brizantha and U. decumbens lying in a previously defined species complex. Crop wild relatives were identified for these clades supporting previous sub-generic groupings in Urochloa based on morphology. Using ancestral trait estimation models, we find that five morphological traits that correlate with forage potential (perennial growth habits, culm height, leaf size, a winged rachis and large seeds) independently evolved in forage clades.

CONCLUSIONS

Urochloa s.l. is a highly diverse genus that contains numerous species with agricultural potential, including crop wild relatives that are currently underexploited. All forage species and their crop wild relatives naturally occur on the African continent and their conservation across their native distributions is essential. Genomic and phenotypic diversity in forage clade species and their wild relatives need to be better assessed both to develop conservation strategies and to exploit the diversity in the genus for improved sustainability in Urochloa cultivar production.

Dynamics of Carbon and Soil Enzyme Activities under Arabica Coffee Intercropped with Brachiaria decumbens in the Brazilian Cerrado

The change in land use in the Brazilian Cerrado modifies the dynamics of soil organic matter (SOM) and, consequently, carbon (C) stocks and their fractions and soil enzyme activities. This study evaluated the effect of brachiaria (Brachiaria decumbens Stapf.) intercropped with Arabica coffee (Coffea arabica L.) on the stock and fractions of soil carbon and enzyme activities. The experiment was arranged in a completely randomized block design with three replications and treatments in a factorial design. The first factor consisted of coffee with or without intercropped brachiaria, the second of Arabica coffee cultivars ('I.P.R.103' and 'I.P.R.99') and the third factor of the point of soil sampling (under the canopy (UC) and in inter-rows (I)). Soil was sampled in layers of 0-10, 10-20, 20-30, 30-40, 40-60 and 60-80 cm. Soil from the 0-10 cm layer was also used to analyze enzymatic activity. Significant effects of coffee intercropped with brachiaria were confirmed for particulate organic carbon (POC), with highest contents in the 0-10 and 20-30 cm layers (9.62 and 6.48 g kg-1, respectively), and for soil enzymes (280.83 and 180.3 μg p-nitrophenol g-1 for arylsulfatase and β-glucosidase, respectively).

Understanding the Relations between Soil Biochemical Properties and N2O Emissions in a Long-Term Integrated Crop-Livestock System

Edaphoclimatic conditions influence nitrous oxide (N2O) emissions from agricultural systems where soil biochemical properties play a key role. This study addressed cumulative N2O emissions and their relations with soil biochemical properties in a long-term experiment (26 years) with integrated crop-livestock farming systems fertilized with two P and K rates. The farming systems consisted of continuous crops fertilized with half of the recommended P and K rates (CCF1), continuous crops at the recommended P and K rates (CCF2), an integrated crop-livestock system with half of the recommended P and K rates (ICLF1), and an integrated crop-livestock at the recommended P and K rates (ICLF2). The ICLF2 may have promoted the greatest entry of carbon into the soil and positively influenced the soil's biochemical properties. Total carbon (TC) was highest in ICLF2 in both growing seasons. The particulate and mineral-associated fractions in 2016 and 2017, respectively, and the microbial biomass fraction in the two growing seasons were also very high. Acid phosphatase and arylsulfatase in ICLF1 and ICLF2 were highest in 2016. The soil properties correlated with cumulative N2O emissions were TC, total nitrogen (TN), particulate nitrogen (PN), available nitrogen (AN), mineral-associated organic carbon (MAC), and microbial biomass carbon (MBC). The results indicated that ICLF2 induces an accumulation of more stable organic matter (OM) fractions that are unavailable to the microbiota in the short term and result in lower N2O emissions.

The Impact Ground Phonolite Rock's Potassium Solubilization in Tropical Soil Depends on the Cultivated Forage Species

Cover crops can be used to accelerate the solubilization process of low-solubility fertilizers; thus, the aim of this study was to evaluate the potential of grasses in solubilizing potassium from phonolite rock powder. With a 2 × 5 factorial scheme, two doses of phonolite rock powder, equivalent to 0 and 8 t ha-1, were combined with four grass species (Urochloa ruziziensis, U. decumbens, U. humidicola, and Andropogon gayanus), besides a control treatment without any cover crop. The dry matter production of the aerial parts of the plants was evaluated at days 40 and 70 post-emergence, and then the concentration of potassium in the plants and the soil was evaluated (exchangeable, non-exchangeable, structural, and total potassium contents). In the soil, the phonolitic rock powder increased the exchangeable, non-exchangeable, structural, and total K contents, favoring the absorption of K and the production of the dry mass of the three Urochloa, but U. decumbens stood out because it promoted greater availability of K in the system compared to the cultivation of other plant species. This research proposes the inclusion of U. decumbens in production systems that receive phonolitic rock, constituting a sustainable strategy to improve its agronomic efficiency.

Crop-livestock-forestry systems as a strategy for mitigating greenhouse gas emissions and enhancing the sustainability of forage-based livestock systems in the Amazon biome

Intensification of livestock systems becomes essential to meet the food demand of the growing world population, but it is important to consider the environmental impact of these systems. To assess the potential of forage-based livestock systems to offset greenhouse gas (GHG) emissions, the net carbon (C) balance of four systems in the Brazilian Amazon Biome was estimated: livestock (L) with a monoculture of Marandu palisade grass [Brachiaria brizantha (Hochst. ex A. Rich.) R. D. Webster]; livestock-forestry (LF) with palisade grass intercropped with three rows of eucalyptus at 128 trees/ha; crop-livestock (CL) with soybeans and then corn + palisade grass, rotated with livestock every two years; and crop-livestock-forestry (CLF) with CL + one row of eucalyptus at 72 trees/ha. Over the four years studied, the systems with crops (CL and CLF) produced more human-edible protein than those without them (L and LF) (3010 vs. 755 kg/ha). Methane contributed the most to total GHG emissions: a mean of 85 % for L and LF and 67 % for CL and CLF. Consequently, L and LF had greater total GHG emissions (mean of 30 Mg CO2eq/ha/year). Over the four years, the system with the most negative net C balance (i.e., C storage) was LF when expressed per ha (-53.3 Mg CO2eq/ha), CLF when expressed per kg of carcass (-26 kg CO2eq/kg carcass), and LF when expressed per kg of human-edible protein (-72 kg CO2eq/kg human-edible protein). Even the L system can store C if well managed, leading to benefits such as increased meat as well as improved soil quality. Moreover, including crops and forestry in these livestock systems enhances these benefits, emphasizing the potential of integrated systems to offset GHG emissions.

Effects of different grassland use patterns on soil bacterial communities in the karst desertification areas

Soil bacteria are closely related to soil environmental factors, and their community structure is an important indicator of ecosystem health and sustainability. A large number of artificial grasslands have been established to control rocky desertification in the karst areas of southern China, but the influence of different use patterns on the soil bacterial community in artificial grasslands is not clear. In this study, three grassland use patterns [i.e., grazing (GG), mowing (MG), and enclosure (EG)] were used to investigate the effects of different use patterns on the soil bacterial community in artificial grassland by using 16S rDNA Illumina sequencing and 12 soil environmental indicators. It was found that, compared with EG, GG significantly changed soil pH, increased alkaline hydrolyzable nitrogen (AN) content (P < 0.05), and decreased soil total phosphorus (TP) content (P < 0.05). However, MG significantly decreased the contents of soil organic carbon (SOC), total phosphorus (TP), available nitrogen (AN), ammonium nitrogen (NH4+-N), β-1,4-glucosidase (BG), and N-acetyl-β-D-glucamosonidase (NAG) (P < 0.05). The relative abundance of chemoheterotrophy was significantly decreased by GG and MG (P < 0.05). GG significantly increased the relative abundance of Acidobacteria and Gemmatimonadota (P < 0.05) and significantly decreased the relative abundance of Proteobacteria (P < 0.05), but the richness index (Chao 1) and diversity index (Shannon) of the bacterial community in GG, MG, and EG were not significantly different (P > 0.05). The pH (R2 = 0.79, P = 0.029) was the main factor affecting the bacterial community structure. This finding can provide a scientific reference for ecological restoration and sustainable utilization of grasslands in the karst desertification areas.

Why is Brachiaria decumbens Stapf. a common species in the mining tailings of the Fundão dam in Minas Gerais, Brazil?

Currently, more than five years after the Fundão dam failure in Mariana, Minas Gerais, Brazil, Brachiaria decumbens Stapf. is the main grass in pasturelands affected by the mining tailings. The aim of this study was to investigate the reason for this fact as well as to determine the ecophysiological effects of mining tailings on B. decumbens and to test whether mixing the tailings with unaffected local soil enhances the affected soil properties. For the experiment, two different soils were collected, one unaffected soil without mining tailings (Ref) and the mining tailings (Tec), and we also created a mixture with 50 % of each soil type (Ref/Tec). We cultivated B. decumbens in the three soil treatments in a greenhouse for 110 days and evaluated soil physical-chemical properties and plant ecophysiology. Our results show that the tailings (Tec) compromised the normal ecophysiological state of B. decumbens. The species survived these adverse conditions due to its great efficiency in acquiring some elements. The soil management tested by this work mitigated the stress caused by tailings and can represent an alternative for the environmental recovery of the affected soils.

Soil microbial nitrogen-cycling gene abundances in response to crop diversification: A meta-analysis

Single planting structure has a significant impact on the maintenance of nitrogen in managed ecosystems. Although the effect of crop diversity on soil nitrogen-cycling microbes is mainly related to the influence of environmental factors, there is a lack of quantitative research. This study aims to determine the effect of diversified cropping mode on the abundance of functional genes in the soil nitrogen cycle based on the quantitative integration of a meta-analysis database containing 189 observation data pairs. The results show that the soil nifH (nitrogenase coding gene), nirS and nirK (nitrite reductase coding gene), and narG (nitrate reductase coding gene) abundances are positively affected by the diversity of plant species, whereas the amoA (ammonia monooxygenase coding gene) and nosZ (nitrous oxide reductase coding gene) show no response. Diversification duration and ecosystem type are important factors that regulate soil nitrogen fixation and nitrification gene abundances. Denitrification genes are mainly affected by categorical variables such as the planting pattern, soil layer, application species, duration, and soil texture. Among them, the long-term continuous diversification is mainly manifested in the reduction of soil nifH and increase of nirK abundances. Soil organic carbon and nitrogen linearly affect the responses of nifH, amoA, nirS, and nirK. Therefore, to maintain the soil ecological function, diversity of planting patterns needs to be applied flexibly by regulating the abundance of nitrogen-cycling genes. Our study draws conclusions in order to provide theoretical references for the sustainability of nitrogen and improvement of management measures in the process of terrestrial managed ecosystem diversification.

C and N stocks in silvopastoral systems with high and low tree diversity: Evidence from a twenty-two year old field study

This paper aimed to quantify the C and N stocks and the natural abundancy of ¹³C (δ¹³C) in organic matter fractions of soil, as well as soil labile C, in a long-term experiment (1997-2019) on silvopastoral systems (SSP) with low and high tree diversity in the Mata Atlântica biome. Disturbed and undisturbed soil samples were collected in transects that were perpendicular to the tree rows every five meters (0, 5, 10, and 15 m of distance), at depths of: 0.0-0.10, 0.10-0.30. 0.30-0.60, 0.60-1.0 m. Litterfall, root density, total organic C and N content, δ¹³C values for particulate organic matter (POM) fractions as well as mineral-associated organic matter (MAOM) and soil labile C, whilst stocks were calculated afterwards. Litterfall production was higher in the high diversity SSP for all distances, except for 5 m from the tree row. In contrast to litterfall, higher root density was observed for the longest tree distances (15 m) in the low diversity system. The high tree diversity SSP increased TOC stocks in the top soil layer (0.0-0.10 m, distances of 0 and 10 m) only and C-MAOM stocks in the surface (0.0-0.10 m, 10 m distance) and subsurface (0.10-0.30 m, 0 m distance). In contrast, total N stocks or stocks associated with MAOM and POM were higher in the high tree diversity system. The increases were of 37, 36 and 63%, respectively, for total N, N-MAOM, and N-POM up to 1 m depth. The smallest δ¹³C values found close to the tree row (0 and 5 m distances), especially in the high diversity system, indicate the influence organic residue from leguminous tree species, whilst the C4 grass held the highest contribution at the 15 m distance, also in the high diversity system. In general, the high diversity tree silvopastoral system has shown potential at storing most C in the 0.0-0.10 m soil layers only and N up to 1 m depth. Results showed very little shift in total C stocks, but the increased N stocks with the inclusion the legumes trees, which is reflected in a lower C:N ratio of the SOM. The silvopastoral system containing signal grass both legumes trees can be looked at as a viable strategy towards sustaining existing soil C stocks, whilst increasing N stocks and SOM quality.

Effect of Cultivated Pastures on Soil Bacterial Communities in the Karst Rocky Desertification Area

Soil bacteria play an important role in regulating the process of vegetation restoration in karst ecosystems. However, the effects of vegetation restoration for different cultivated pastures on soil bacterial communities in the karst rocky desertification regions remain unclear. Therefore, we hypothesized that mixed pasture is the most effective for soil bacterial communities among different vegetation restorations. In this study, we systematically studied the soil properties and soil bacterial communities in four vegetation restoration modes [i.e., Dactylis glomerata pasture (DG), Lolium perenne pasture (LP), Lolium perenne + Trifolium repens mixed pasture (LT), and natural grassland (NG)] by using 16S rDNA Illumina sequencing, combined with six soil indicators and data models. We found that the vegetation restoration of cultivated pastures can improve the soil nutrient content compared with the natural grassland, especially LT treatment. LT treatment significantly increased the MBC content and Shannon index. The vegetation restoration of cultivated pastures significantly increased the relative abundance of Proteobacteria, but LT treatment significantly decreased the relative abundance of Acidobacteria. Soil pH and MBC significantly correlated with the alpha diversity of soil bacterial. Soil pH and SOC were the main factors that can affect the soil bacterial community. FAPROTAX analysis showed LT treatment significantly decreased the relative abundance of aerobic chemoheterotrophs. The results showed that the bacterial communities were highly beneficial to soil restoration in the LT treatment, and it confirmed our hypothesis. This finding provides a scientific reference for the restoration of degraded ecosystems in karst rocky desertification areas.

Growth, Nutrient Accumulation, and Nutritional Efficiency of a Clonal Eucalyptus Hybrid in Competition with Grasses

Invasive grasses reduce resource availability, mainly nutrients in the soil, and the growth of eucalyptus plants. Efficient management to increase productivity depends on understanding levels of weed interference in eucalyptus plantations. The nutritional efficiency of eucalyptus plants in competition has been evaluated by plant tissue analysis. The objective was to evaluate the growth, relative accumulation of nutrients, and nutritional efficiency of the eucalyptus clonal hybrid I144 (Eucalyptus urophylla × Eucalyptus grandis), in competition with Megathyrsus maximus cv. BRS zuri, Urochloa brizantha cv. marandu, Urochloa decumbens cv. basilisk and in the control (eucalyptus plants without weed competition). The experiment was carried out with a completely randomized design, with four treatments and ten replications. The height, stem diameter, number of leaves, leaf area, dry matter of leaves and stem, nutrient content in leaves and uptake, transport, and N, P, and K utilization efficiency of the eucalyptus clonal hybrid were evaluated at 110 days after transplantation. The growth parameters and relative contents of macro and micronutrients in the eucalyptus clonal hybrid were lower in competition with M. maximus, U. brizantha and U. decumbens. The efficiency of N, P, and K uptake and transport by the eucalyptus clonal hybrid was 29.41 and 7.32% lower in competition with U. decumbens than in the control treatments, respectively. The efficiency of N, P, and K utilization by eucalypts was 13.73, 9.18, and 22.54% lower in competition with M. maximus, U. brizantha, and U. decumbens, respectively. The reduced growth and nutritional parameters of the eucalyptus clonal hybrid were more evident in competition with U. decumbens. Plant tissue analyses efficiently determined the level of competition for nutrients between species. Crop competition with grasses can decrease the efficiency and use of nutrients, which consequently reduces plant development and productivity.

Tapping Into the Environmental Co-benefits of Improved Tropical Forages for an Agroecological Transformation of Livestock Production Systems

Livestock are critical for incomes, livelihoods, nutrition and ecosystems management throughout the global South. Livestock production and the consumption of livestock-based foods such as meat, cheese, and milk is, however, under global scrutiny for its contribution to global warming, deforestation, biodiversity loss, water use, pollution, and land/soil degradation. This paper argues that, although the environmental footprint of livestock production presents a real threat to planetary sustainability, also in the global south, this is highly contextual. Under certain context-specific management regimes livestock can deliver multiple benefits for people and planet. We provide evidence that a move toward sustainable intensification of livestock production is possible and could mitigate negative environmental impacts and even provide critical ecosystem services, such as improved soil health, carbon sequestration, and enhanced biodiversity on farms. The use of cultivated forages, many improved through selection or breeding and including grasses, legumes and trees, in integrated crop-tree-livestock systems is proposed as a stepping stone toward agroecological transformation. We introduce cultivated forages, explain their multi-functionality and provide an overview of where and to what extent the forages have been applied and how this has benefited people and the planet alike. We then examine their potential to contribute to the 13 principles of agroecology and find that integrating cultivated forages in mixed crop-tree-livestock systems follows a wide range of agroecological principles and increases the sustainability of livestock production across the globe. More research is, however, needed at the food system scale to fully understand the role of forages in the sociological and process aspects of agroecology. We make the case for further genetic improvement of cultivated forages and strong multi-disciplinary systems research to strengthen our understanding of the multidimensional impacts of forages and for managing agro-environmental trade-offs. We finish with a call for action, for the agroecological and livestock research and development communities to improve communication and join hands for a sustainable agri-food system transformation.

Flow Cytometry-Based Determination of Ploidy from Dried Leaf Specimens in Genomically Complex Collections of the Tropical Forage Grass Urochloa s. l

Urochloa (including Brachiaria, Megathyrus and some Panicum) tropical grasses are native to Africa and are now, after selection and breeding, planted worldwide, particularly in South America, as important forages with huge potential for further sustainable improvement and conservation of grasslands. We aimed to develop an optimized approach to determine ploidy of germplasm collection of this tropical forage grass group using dried leaf material, including approaches to collect, dry and preserve plant samples for flow cytometry analysis. Our methods enable robust identification of ploidy levels (coefficient of variation of G0/G1 peaks, CV, typically <5%). Ploidy of some 348 forage grass accessions (ploidy range from 2x to 9x), from international genetic resource collections, showing variation in basic chromosome numbers and reproduction modes (apomixis and sexual), were determined using our defined standard protocol. Two major Urochloa agamic complexes are used in the current breeding programs at CIAT and EMBRAPA: the 'brizantha' and 'humidicola' agamic complexes are variable, with multiple ploidy levels. Some U. brizantha accessions have odd level of ploidy (5x), and the relative differences in fluorescence values of the peak positions between adjacent cytotypes is reduced, thus more precise examination of this species is required. Ploidy measurement of U. humidicola revealed aneuploidy.