Aim
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.
Methods
Soil nitrification rates and BNI potential in root-tissue were analyzed in a hybrid population (117), obtained from two contrasting Bh parents, namely CIAT 26146 and CIAT 16888, with low and high BNI activity, respectively. Observed BNI activity was validated by measuring archaeal (AOA) and bacterial (AOB) nitrifier abundance in the rhizosphere soil of parents and contrasting hybrids. Comparisons of the BNI potential of four forage grasses were conducted to evaluate the feasibility of using nitrification rates to measure BNI activity under field and pot grown conditions.
Results
High BNI activity was the phenotype most commonly observed in the hybrid population (72%). BNI activity showed a similar tendency for genotypes grown in pots and in the field. A reduction in AOA abundance was found for contrasting hybrids with low nitrification rates and high BNI potential.
Conclusion
Bh hybrids with high levels of BNI activity were identified. Our results demonstrate that the microcosm incubation and the in vitro bioassay may be used as complementary methods for effectively assessing BNI activity. The full expression of BNI potential of Bh genotypes grown in the soil (i.e. low nitrification rates) requires up to one year to develop, after planting.
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 ~ 20 μg mL−1, ED80 ~ 40 μg mL−1), followed by compound 4 with intermediate (ED50 ~ 40 μg 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.
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•B. humidicola root exudates reveal undescribed brachialactone isomers and derivatives.•3-epi-brachialactone shows highest biological activity (nitrification inhibition).•Stereochemistry at C3 is of high relevance for biological activity of fusicoccanes.•A similar mode of action of fusicoccanes in plants and microorganisms is suggested.
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 Tacuarí (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 Tacuarí 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.
Modern intensively managed pastures that receive large external nitrogen (N) inputs account for high N losses in form of nitrate (NO
3
–
) leaching and emissions of the potent greenhouse gas nitrous ...oxide (N
2
O). 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), N
2
O 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 N
2
O 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 N
2
O 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 N
2
O emissions and their relationship with productivity and forage quality, pointing a way to develop N conservative improved forage grasses for tropical livestock production.
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 (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 in carbon‐climate feedback projections.
Soils samples along geothermal gradients (at 2, 10 and 30 m from a geothermally active zone) of increasing mean annual temperature (MAT) in two biomes (kanuka stand and grassland) presented shifts in the composition of microbial communities (as shown by the non‐parametric multidimensional scaling (MDS) plots), but similar relative temperature sensitivities (Q10). The temperature sensitivity was however correlated with the carbon content of soil samples, which varied independently from temperature. The results suggest that while long‐term warming selects for warm‐adapted taxa, substrate quantity exerts a stronger influence than temperature in selecting for distinct thermal traits.
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.
•Biological fixation is the largest input of nitrogen (N) to non-irrigated and irrigated lucerne.•N leaching is 1.5–15 times greater under irrigated relative to non-irrigated lucerne.•N leaching is 3 times greater under grazing compared to cut-and-carry management.•Irrigation increases N outputs to a greater extent than inputs, affecting the soil N balance.
ABSTRACT
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.
Distribution and network properties of multi-kingdom communities (prokaryotes, fungi, protists and nematodes) along a deep soil profile in a pastoral ecosystem.
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.
•NRA in leaves can serve as an indicator of in vivo BNI activity in soils by Bh.•Potential soil nitrification rates correlated positively with measured leaf NRA.•High BNI potentials were indicated by low leaf NRA and low leaf δ15N signatures.•Leaf NRA correlated with soil NO3− contents of contrasting Bh genotypes.•NRA was detected in Bh leaves rather than roots, regardless of NO3− availability.
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.
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 13C 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 13C enriched substrates, suggesting preferential stabilisation of plant‐derived (13C 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 13C 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.
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