In the low fertility acid soils of the Orinoquian savannas of Colombia, Urochloa humidicola cv. Tully or Humidicola is one of the most widely planted tropical forage grasses for improving livestock productivity. Low nutritional quality of this grass limits sustainable livestock production in this region. In this study, we conducted a phenotypic evaluation under field and greenhouse conditions of one of the first hybrid populations of U. humidicola generated from the forage breeding program of CIAT. Our objective was to identify a set of new hybrids of U. humidicola that combine improved productivity and nutritional quality plus the biological nitrification inhibition (BNI) trait/ability to reduce nitrogen (N) losses via leaching and nitrous oxide (N2O) emissions. To this end, we tested 118 hybrids (planted in pots) in the greenhouse for over 6 months and measured potential nitrification rates (NR) using soil microcosm incubation. NR values observed ranged from 0.27 to 5.75 mg N-NO3- kg soil(-1) day(-1). Later, 12 hybrids with different levels of NR were selected and field-tested in the Orinoquia region over a 4 years period (2013-2017) for dry matter production, nutrition quality (crude protein, in vitro digestibility and fibres content) and NR in each year. In the rainy season of 2018, two hybrids with superior agronomic performance and contrasting field level NR (Uh08/1149 and 0450) were subjected to analysis of soil-borne N2O emissions after fertilization during 13 days. The NR values recorded were not directly correlated with the forage quality parameters evaluated, however, the two grasses with the lowest NR values were among those with the highest biomass production, crude protein content, and N uptake. The grass hybrid Uh08/1149 and the germplasm accession CIAT 16888 were found as materials with superior forage value, with production of 14.1 and 14.6 tons dry matter ha(-1) year(-1) (up to 8% higher than the cv. Tully), crude protein of 11.5 and 9.1% per cut (up to 20% higher than the cv. Tully), and N uptake of 31.6 and 25.7 kg N ha(-1) cut(-1) (up to 30% higher than the cv. Tully). Additionally, these two grasses are likely to exhibit high-BNI ability, with potential to improve N use efficiency in managed pastures.

Climate warming may be exacerbated if rising temperatures stimulate losses of soil carbon to the atmosphere. Despite a plethora of studies stimulated by this alarming perspective, the direction and magnitude of this so-called carbon-climate feedback remain uncertain. Part of the uncertainty is due to lack of knowledge of the thermal adaptation of the physiology and composition of soil microbial communities. Here, we tested the hypothesis that microbial communities adapt to long-term warming with a shift in their composition and their temperature response that are consistent with evolutionary theory. We used the unique combination of state-of-the-art macromolecular rate theory (MMRT) to describe the temperature response of microbial respiration and metabarcoding to characterise the microbial community composition of soils sampled along transects of increasing distance from a geothermally active zone in New Zealand. Along those transects, the mean annual temperature of the soil increased dramatically (by up to 15oC), and this concurred with shifts in microbial communities composition, with thermophile and thermotolerant genera increasing in relative abundance with increasing ambient temperature. However, the ambient temperature had no detectable influence on the MMRT parameters or the relative temperature sensitivity of decomposition (Q10). MMRT parameters were, however, strongly correlated with soil carbon concentration and carbon:nitrogen ratio. Our findings suggest that, while long-term warming selects for warm-adapted taxa, substrate quality and quantity exert a stronger influence than temperature in selecting for distinct thermal traits. The results have major implications for our understanding of the role of soil microbial processes in the long-term effects of climate warming on soil carbon dynamics and will help increase confidence carbon-climate feedback projections.

Intensification of agricultural management practices, including irrigation and addition of nitrogen (N) fertilizers, can lead to enhanced N leaching and loss of soil fertility. In New Zealand, expansion of the dairy industry has rapidly increased irrigated land area, particularly on shallow, stony soils of the Canterbury region that are prone to leaching, leading to degradation of surface- and ground-water quality and losses of soil N and carbon (C). In this study, we measure components of N balance for two adjacent fields of lucerne (Medicago sativa L., alfalfa) harvested for cut-and-carry feed and grazed in situ. One field was non-irrigated and one irrigated with both water and dairy effluent. Inputs from N fixation associated with the legume crop were quantified using a natural abundance isotopic approach. Drainage from the root zone and leaching were measured with 6 large lysimeters in each field. Leaching losses from non-irrigated lucerne were 7-30 kg N ha(-1) y(-1) with the largest losses occurring in a year with primarily grazing management. Losses from irrigated lucerne were 39-102 kg N ha(-1) y(-1) , with the largest losses resulting from summer drainage events exacerbated by irrigation. Fixation of N was the largest input to both systems, contributing 192-257 kg N ha(-1) y(-1) for non-irrigated lucerne. Under irrigation, biomass production increased, but N uptake from effluent and soil stocks contributed to biomass N to a greater extent and fixation was 262-286 kg N ha(-1) y(-1) . Management influenced N balance through inputs from animal excreta and effluent additions and exports through harvest and grazing removals. Management practices which reduce N losses from the soil are needed to minimize environmental impacts and protect soil fertility.

There is increasing evidence that the accessibility of soil organic matter (SOM) to microbial decomposers is more important than chemical recalcitrance for regulating SOM stability. We show that the rapid reduction in SOM decomposition following the addition of sorptive mineral phases to soils in laboratory conditions leads to decreased accessibility of SOM to microbial decomposers due to the formation of organo-mineral complexes. We manipulated SOM accessibility in a short-term microcosm experiment by adding different proportions of a sorptive mineral material derived from an aluminium-rich allophanic soil to a constant mass of soil to determine the effects on SOM decomposition after 1, 4 and 8 days. The decrease in SOM decomposition with increasing proportion of added sorptive mineral phase occurred within 1 day and did not change further at 4 and 8 days. In a second experiment, we added three proportions of the sorptive mineral phases (0%, 15% and 50%) to three soils with different carbon (C) concentrations and measured rates of SOM decomposition, changes in water extractable C, the formation of organo-mineral complexes inferred from pyrophosphate-extractable aluminium, and the natural abundance C-13 isotopic composition of CO2 derived from SOM decomposition. We confirmed that the proportional decreases in SOM decomposition with increasing organo-mineral complexes and decreasing microbial access to SOM was the same for the three soils, suggesting that the effects are independent of soil C concentration and pH. We also showed that the short-term reductions in SOM accessibility led to microbial decomposition of more C-13 enriched substrates, suggesting preferential stabilisation of plant-derived (C-13 depleted) substrates. Our study demonstrated that SOM accessibility and decomposition could be reduced rapidly and proportionally to the amount of added sorptive mineral phases resulting from increased organo-mineral interactions irrespective of the initial soil organic carbon concentration. Highlights Addition of sorptive mineral phases reduced short-term soil organic matter (SOM) decomposition by the same proportion for three soils. Relatively C-13 depleted SOM was preferentially adsorbed onto the mineral phases. The reduction in SOM decomposition was attributed to reduced microbial access due to increased organo-mineral interactions. The effects occurred rapidly and proportionally to the amount of added sorptive mineral phases.

Nitrogen (N) inputs to agricultural systems contribute substantially to soil nitrate (NO3−) concentrations, which increase NO3− leaching and contamination of groundwater. The influence of soil microbes in regulating NO3− concentrations in the topsoil are well studied but it is often assumed that microbial regulation of NO3− concentrations in the subsoil is negligible. The aim of this study was to test this assumption by determining the relationships between microbial properties and NO3− concentrations in both the subsoil and the topsoil. We measured the size of the mineralizable N (Nm) pool, microbial properties (microbial biomass, bacterial richness), nitrifier gene abundance (amoA gene copy number), denitrifier gene abundance (nirK and nirS gene copy number), denitrifier enzyme activity and NO3− concentrations in the topsoil and the subsoil in a well-drained stony soil under an established lucerne crop. We used structural equation modelling (SEM) to identify and compare the linkages of microbial properties with NO3− concentrations at each depth. In the topsoil, we found higher Nm, gene abundance, denitrification enzyme activity, bacterial richness, and microbial biomass than those in the subsoil, but there were no relationships between these variables and NO3− concentrations in the topsoil (the SEM model explained 0.06% of the variability in NO3− concentrations). In contrast, in the subsoil, NO3− concentrations were strongly correlated with bacterial amoA abundance and denitrification enzyme activity, with both variables associated significantly with Nm. We found that bacterial richness was also associated with Nm in the subsoil. Our findings highlight that microbial properties are associated with NO3− concentrations in the subsoil (the SEM model explained 82% the variability in NO3− concentrations) and this suggest that nitrification and denitrification may contribute to regulating NO3− concentrations in the subsoil. Our findings also suggest that denitrification contributes to reducing NO3− concentrations in the subsoil. We conclude that studies addressing drivers of NO3− leaching need to consider the potential for microbially-mediated attenuation (or an increase) in NO3− concentrations throughout the soil profile.

>Dear Editor,Approximately 55% of the agricultural land in New Zealand is grazed grassland to support the expanding dairy and meat industries. Intensified management practices such as irrigation, nitrogen (N) fertiliser application,

Climate warming may be exacerbated if rising temperatures stimulate losses of soil carbon to the atmosphere. The direction and magnitude of this carbon‐climate feedback are uncertain, largely due to lack of knowledge of the thermal adaptation of the physiology and composition of soil microbial communities. Here, we applied the macromolecular rate theory (MMRT) to describe the temperature response of the microbial decomposition of soil organic matter (SOM) in a natural long‐term warming experiment in a geothermally active area in New Zealand. Our objective was to test whether microbial communities adapt to long‐term warming with a shift in their composition and their temperature response that are consistent with evolutionary theory of trade‐offs between enzyme structure and function. We characterized the microbial community composition (using metabarcoding) and the temperature response of microbial decomposition of SOM (using MMRT) of soils sampled along transects of increasing distance from a geothermally active zone comprising two biomes (a shrubland and a grassland) and sampled at two depths (0–50 and 50–100 mm), such that ambient soil temperature and soil carbon concentration varied widely and independently. We found that the different environments were hosting microbial communities with distinct compositions, with thermophile and thermotolerant genera increasing in relative abundance with increasing ambient temperature. However, the ambient temperature had no detectable influence on the MMRT parameters or the relative temperature sensitivity of decomposition ( Q 10 ). MMRT parameters were, however, strongly correlated with soil carbon concentration and carbon:nitrogen ratio. Our findings suggest that, while long‐term warming selects for warm‐adapted taxa, substrate quality and quantity exert a stronger influence than temperature in selecting for distinct thermal traits. The results have major implications for our understanding of the role of soil microbial processes in the long‐term effects of climate warming on soil carbon dynamics and will help increase confidence in carbon‐climate feedback projections.

Rice root exudates can control nitrification by releasing biological nitrification inhibitors (BNIs), reducing nitrogen losses in agricultural soils. However, the inhibitory effect on nitrification and the abundance of ammonia oxidisers in different soil types remain unclear. Two temperate paddy soils with different organic matter contents were collected to investigate the impact on nitrification rates of two rice cultivar root exudates, El Paso 144 (O. sativa ssp. indica) and Tacuari (O. sativa spp. japonica). Root exudates were extracted before the tillering growth stage, and their BNI potential was evaluated in a bioassay with luminescent Nitrosomonas europaea and in a 12-day soil microcosm incubation. While exudates from Tacuari showed stronger BNI activity in the bioassay, its nitrification inhibition in both soils was similar to that of DCD. El Paso did not show BNI activity in Salto whose organic matter content was higher. The abundance of ammonia oxidisers was not affected by root exudates or DCD, but only ammonia-oxidising bacteria had a significant positive relationship with soil nitrate. Our results demonstrated that although the bioassay showed high BNI activity, its expression in soils varied depending on the rice cultivar and the type of soil, particularly with its organic matter content.

The biodiversity and structure of deep agricultural soil communities are poorly understood, especially for eukaryotes. Using DNA metabarcoding and co-occurrence networks, we tested whether prokaryote, fungal, protist, and nematode biodiversity declines with increasing depth (0-0.1, 0.3-0.5, and 1.1-1.7m) in pastoral soil; whether deep soil organisms are subsets of those at the surface; and whether multi-kingdom networks become more interconnected with increasing depth. Depth-related richness declines were observed for almost all detected fungal classes, protist phyla, and nematode orders, but only 13 of 25 prokaryote phyla, of which nine had increasing richness with depth. Deep soil communities were not simply subsets of surface communities, with 3.8%-12.2% of eukaryotes and 13.2% of prokaryotes detected only in the deepest samples. Eukaryotes mainly occurred in the upper soil layers whereas prokaryotes were more evenly distributed across depths. Plant-feeding nematodes were most abundant in top soil, whereas bacteria feeders were more abundant in deep soil. Co-occurrence network structure differences suggested that deep soil communities are concentrated around scarce niches of resource availability, in contrast to more spatially homogenous and abundant resources at the surface. Together, these results demonstrate effects of depth on the composition, distribution, and structure of prokaryote and eukaryote soil communities.

Coffee berry borer-CBB (Hypothenemus hampei) is a globally important economic pest of coffee (Coffea spp.). Despite current insect control methods for managing CBB, development of future control strategies requires a better understanding of its biology and interaction with its host plant. Towards this objective, we performed de novo CBB genome and transcriptome sequencing, improved CBB genome assembly and predicted 18,765 protein-encoding genes. Using genome and transcriptome data, we annotated the genes associated with chemosensation and found a reduced gene repertoire composed by 67 odorant receptors (ORs), 62 gustatory receptors (GRs), 33 ionotropic receptors (IRs) and 29 odorant-binding proteins (OBPs). In silico transcript abundance analysis of these chemosensory genes revealed expression enrichment in CBB adults compared with larva. Detection of differentially expressed chemosensory genes between males and females is likely associated with differences in host-finding behavior between sexes. Additionally, we discovered male-specific genome content and identified candidate male-specific expressed genes on these scaffolds, suggesting that a Y-like chromosome may be involved in the CBB's functional haplodiploid mechanism of sex determination.

Modern intensively managed pastures that receive large external nitrogen (N) inputs account for high N losses in form of nitrate (NO3-) leaching and emissions of the potent greenhouse gas nitrous oxide (N2O). The natural plant capacity to shape the soil N cycle through exudation of organic compounds can be exploited to favor N retention without affecting productivity. In this study, we estimated the relationship between biological nitrification inhibition (BNI), N2O emissions and plant productivity for 119 germplasm accessions of Guineagrass (Megathyrsus maximus), an important tropical forage crop for livestock production. This relation was tested in a greenhouse experiment measuring BNI as (i) rates of soil nitrification; (ii) abundance of ammonia-oxidizing bacteria (AOB) and archaea (AOA); and (iii) the capacity of root tissue extracts to inhibit nitrification in vitro. We then measured N2O emissions, aboveground biomass and forage nutrition quality parameters. Reductions on nitrification activity ranging between 30 and 70% were found across the germplasm collection of M. maximus. Accessions with low nitrification rates showed a lower abundance of AOB as well as a reduction in N2O emissions compared to accessions of high nitrification rates. The BNI capacity was not correlated to N uptake of plants, suggesting that there may be intraspecific variation in the exploitation of different N sources in this grass species. A group of accessions (cluster) with the most desirable agronomic and environmental traits among the collection was identified for further field validation. These results provide evidence of the ability of M. maximus to suppress soil nitrification and N2O emissions and their relationship with productivity and forage quality, pointing a way to develop N conservative improved forage grasses for tropical livestock production.

Biological Nitrification Inhibition (BNI) of Brachiaria humidicola has been mainly attributed to the root-exuded fusicoccane-type diterpene brachialactone. We hypothesized, however, that according to the high diversity of fusicoccanes described for plants and microorganisms, BNI of B. humidicola is caused by an assemblage of bioactive fusicoccanes. B. humidicola root exudates were collected hydroponically and compounds isolated by semi-preparative HPLC. Chemical structures were revealed by spectroscopic techniques, including HRMS as well as 1D and 2D NMR. Nitrification inhibiting (NI) potential of isolated compounds was evaluated by a Nitrosomonas europaea based bioassay. Besides the previously described brachialactone (1), root exudates contained 3-epi-brachialactone (2), the C3-epimer of 1 (m/z 334), as well as 16-hydroxy-3-epi-brachialactone (3) with an additional hydroxyl group at C16 (m/z 350) and 3,18-epoxy-9-hydroxy-4,7-seco-brachialactone (4), which is a ring opened brachialactone derivative with a 3,18 epoxide ring and a hydroxyl group at C9 (m/z 332). The 3-epi-brachialactone (2) showed highest NI activity (ED50 similar to 20 mu g mL(-1), ED80 similar to 40 mu g mL(-1)), followed by compound 4 with intermediate (ED50 similar to 40 mu g mL(-1)) brachialactone (1) with low and compound 3 without activity. In coherence with previous reports on fusicoccanes, stereochemistry at C3 was of high relevance for the biological activity (NI potential) of brachialactones.

The use of tropical grasslands to graze livestock is of high economic importance. Declining grassland soil health leads to reduced sustainability of livestock systems. There are high levels of phenotypic diversity amongst tropical forage grasses. We hypothesise that this variation could lead to significant differences in soil health and that selection of forage cultivars to improve soil health could improve the sustainability of livestock production. We measured and compared key soil health metrics (soil organic carbon (SOC) concentration and sugar / alkane composition, aggregate stability, friability, litter decomposition rates, microbial community composition) under four tropical forage varieties (Brachiaria hybrid cv Mulato (BhMulato), B. humidicola cv Tully (CIAT679; Bh679), B. humidicola cv CIAT16888 (Bh16888), and Panicum maximum CIAT 6962 (Pmax)) and a bare soil control, there was a significant difference in soil aggregate stability, friability and SOC concentration between the forage varieties with soil under Bh679 and Bh16888 tending to have greater aggregate stability, friability and SOC concentrations compared to the soil under BhMulato and Pmax. We identified significant spatial variation in soils under BhMulato and Pmax due to their tussock forming growth habit; when compared to soil from adjacent to the tussocks, soil from the gaps between tussocks had significantly reduced aggregate stability under both species, significantly reduced friability under Pmax and significantly reduced SOC under BhMulato. We found limited impact of forage variety on soil microbial community composition, litter decomposition rates or soil alkane and sugar concentrations.

The tropical forage grass Brachiaria humidicola (Bh) controls soil microbial nitrification via biological nitrification inhibition (BNI). The aim of our study was to verify if nitrate reductase activity (NRA) in Bh roots or leaves reflects in vivo performance of BNI in soils. NRA was measured in roots and leaves of contrasting accessions and apomictic hybrids of Bh grown under controlled greenhouse and natural field conditions. Nitrate (NO3−) contents were measured in soil solution and in Bh stem sap to validate NRA data. Potential soil nitrification rates (NRs) and leaf δ15N values were used to verify in vivo BNI by the NRA assay in the field study. NRA was detected in Bh leaves rather than roots, regardless of NO3− availability. NRA correlated with NO3− contents in soils and stem sap of contrasting Bh genotypes substantiating its reflectance of in vivo BNI performance. Additionally, leaf NRA data from the field study significantly correlated with simultaneously collected NRs and leaf δ15N data. The leaf NRA assay facilitated a rapid screening of contrasting Bh genotypes for their differences in in vivo performance of BNI under field and greenhouse conditions, but inconsistency of the BNI potential by Bh germplasm was observed. Among Bh genotypes tested, leaf NRA was closely linked with nitrification activity, and consequently with actual BNI performance. It was concluded that NRA in leaves of Bh can serve as an indicator of in vivo BNI activity when complemented with established BNI methodologies (δ15N, NRs) under greenhouse and field conditions.

Utilization of biological nitrification inhibition (BNI) strategy can reduce nitrogen losses in agricultural systems. This study is aimed at characterizing BNI activity in a plant-soil system using a biparental hybrid population of Brachiaria humidicola (Bh), a forage grass with high BNI potential but of low nutritional quality.

The tropical forage grass Brachiaria humidicola (Bh) suppresses the activity of soil nitrifiers through biological nitrification inhibition (BNI). As a result, nitrate ( NO 3 - ) formation and leaching are reduced which is also expected to tighten the soil nitrogen (N) cycle. However, the beneficial relationship between reduced NO 3 - losses and enhanced N uptake due to BNI has not been experimentally demonstrated yet. Nitrification discriminates against the 15N isotope and leads to 15N depleted NO 3 - , but 15N enriched NH 4 + in soils. Leaching of 15N depleted NO 3 - enriches the residual N pool in the soil with 15N. We hypothesized that altered nitrification and NO 3 - leaching due to diverging BNI magnitudes in contrasting Bh genotypes influence soil 15N natural abundance (δ15N), which in turn is reflected in distinct δ15N in Bh shoot biomass. Consequently, high BNI was expected to be reflected in low plant δ15N of Bh. It was our objective to investigate under controlled conditions the link between shoot value of δ15N in several Bh genotypes and leached NO 3 - amounts and shoot N uptake. Additionally, plant 15N and N% was monitored among a wide range of Bh genotypes with contrasting BNI potentials in field plots for 3 years. We measured leaf δ15N of young leaves (regrown after cutback) of Bh and combined it with nitrification rates (NRs) of incubated soil to test whether there is a direct relationship between plant δ15N and BNI. Increased leached NO 3 - was positively correlated with higher δ15N in Bh, whereas the correlation between shoot N uptake and shoot δ15N was inverse. Field cultivation of a wide range of Bh genotypes over 3 years decreased NRs in incubated soil, while shoot δ15N declined and shoot N% increased over time. Leaf δ15N of Bh genotypes correlated positively with NRs of incubated soil. It was concluded that decreasing plant δ15N of Bh genotypes over time reflects the long-term effect of BNI as linked to lower NO 3 - formation and reduced NO 3 - leaching. Accordingly, a low δ15N in Bh shoot tissue verified its potential as indicator of high BNI activity of Bh genotypes.

High nitrogen (N) concentration in bovine urine, which generally exceeds plant N uptake rates, results in the formation of hotspots of N loss when bovine urine is deposited on grazed pasture soils. High spatial variability in the distribution of urine patches in grazed pastures poses a major challenge to mitigate N losses. Some exudates from the roots of several tropical forage grasses were shown to inhibit the activity of soil nitrifiers; a process known as biological nitrification inhibition (BNI). We hypothesized that nitrate (NO3−) production and nitrous oxide (N2O) emissions from urine patches deposited on soils under forage grasses with high BNI capacity are lower than those with forage grasses with low BNI capacity. This hypothesis was tested using field plots of two tropical forage grass cultivars, Brachiaria humidicola cv. Tully (BT) and interspecific Brachiaria hybrid cv. Mulato (BM) which, correspondingly, have high and low BNI capacity. Nitrification rates and amoA gene copy numbers of ammonia oxidizing archaea (AOA) and bacteria (AOB) in soils under the two forage grasses were quantified before and after urine and water (control) application, as well, an additional experiment was conducted to quantify denitrification potential. Moreover, soil N2O emissions from simulated urine (0.123 kg N m−2) and water patches were monitored over a 29-day period. Results showed a greater suppression of nitrification, denitrification and AOA abundance in soils under BT than those under BM. Positive relationships (p < 0.05) existed between AOA and AOB abundance and NO3− contents in soils under BM. Bovine urine resulted in higher cumulative N2O fluxes from soils under BM (80 mg N2O-N m−2) compared to those under BT (32 mg N2O-N m−2). Consequently, N2O emission factors were higher for soils under BM (0.07%) than under BT (0.00002%). We conclude that tropical forage grasses with high BNI capacity play a key role in mitigating N2O emissions from bovine urine patches in archaea-dominated soils. This suggests that wide-spread adoption of tropical forage grasses with high BNI capacity may have a great potential to tighten N cycling in grazed pastures.

The coffee berry borer (CBB) Hypothenemus hampei is the most limiting pest of coffee production worldwide. The CBB genome has been recently sequenced; however, information regarding the presence and characteristics of transposable elements (TEs) was not provided. Using systematic searching strategies based on both de novo and homology-based approaches, we present a library of TEs from the draft genome of CBB sequenced by the Colombian Coffee Growers Federation. The library consists of 880 sequences classified as 66% Class I (LTRs: 46%, non-LTRs: 20%) and 34% Class II (DNA transposons: 8%, Helitrons: 16% and MITEs: 10%) elements, including families of the three main LTR (Gypsy, Bel-Pao and Copia) and non-LTR (CR1, Daphne, I/Nimb, Jockey, Kiri, R1, R2 and R4) clades and DNA superfamilies (Tc1-mariner, hAT, Merlin, P, PIF-Harbinger, PiggyBac and Helitron). We propose the existence of novel families: Hypo, belonging to the LTR Gypsy superfamily; Hamp, belonging to non-LTRs; and rosa, belonging to Class II or DNA transposons. Although the rosa clade has been previously described, it was considered to be a basal subfamily of the mariner family. Based on our phylogenetic analysis, including Tc1, mariner, pogo, rosa and Lsra elements from other insects, we propose that rosa and Lsra elements are subfamilies of an independent family of Class II elements termed rosa. The annotations obtained indicate that a low percentage of the assembled CBB genome (approximately 8.2%) consists of TEs. Although these TEs display high diversity, most sequences are degenerate, with few full-length copies of LTR and DNA transposons and several complete and putatively active copies of non-LTR elements. MITEs constitute approximately 50% of the total TEs content, with a high proportion associated with DNA transposons in the Tc1-mariner superfamily.

Agricultural producers grapple with low farm yields and declining ecosystem services within their landscapes. In several instances, agricultural production systems may be considered largely unsustainable in socioeconomic and ecological (resource conservation and use and impact on nature) terms. Novel technological and management options that can serve as vehicles to promote the provision of multiple benefits, including the improvement of smallholder livelihoods, are needed. We call for a paradigm shift to allow designing and implementing agricultural systems that are not only efficient (serving as a means to promote development based on the concept of creating more goods and services while using fewer resources and creating less waste) but can also be considered synergistic (symbiotic relationship between socio-ecological systems) by simultaneously contributing to major objectives of economic, ecological, and social (equity) improvement of agro-ecosystems. These transformations require strategic approaches that are supported by participatory system-level research, experimentation, and innovation. Using data from several studies, we here provide evidence for technological and management options that could be optimized, promoted, and adopted to enable agricultural systems to be efficient, effective, and, indeed, sustainable. Specifically, we present results from a study conducted in Colombia, which demonstrated that, in rice systems, improved water management practices such as Alternate Wetting and Drying (AWD) reduce methane emissions (~70%). We also show how women can play a key role in AWD adoption. For livestock systems, we present in vitro evidence showing that the use of alternative feed options such as cassava leaves contributes to livestock feed supplementation and could represent a cost-effective approach for reducing enteric methane emissions (22% to 55%). We argue that to design and benefit from sustainable agricultural systems, there is a need for better targeting of interventions that are co-designed, co-evaluated, and co-promoted, with farmers as allies of transformational change (as done in the climate-smart villages), not as recipients of external knowledge. Moreover, for inclusive sustainability that harnesses existing knowledge and influences decision-making processes across scales, there is a need for constant, efficient, effective, and real trans-disciplinary communication and collaboration.

The forage grass Brachiaria humidicola (Bh) has been shown to reduce soil microbial nitrification. However, it is not known if biological nitrification inhibition (BNI) also has an effect on nitrogen (N) cycling during cultivation of subsequent crops. Therefore, the objective of this study was to investigate the residual BNI effect of a converted long-term Bh pasture on subsequent maize (Zea mays L.) cropping, where a long-term maize monocrop field (M) served as control.