To achieve a world without hunger, it is imperative to address the inefficiencies within the current agricultural system by adopting innovative and sustainable approaches. One such approach involves ...the use of graphene-based nanomaterials (GNMs), which have shown potential in alleviating plant stress, improving the performance of agrochemicals, enhancing fertilizer retention in the soil, and positively affecting plant productivity. This review explores the potential of GNMs as amendments in conventional agricultural practices and discusses the interactions with both biotic and abiotic components present in agriculture. Analysis of the literature showed that the biocidal action of GNMs in a complex soil matrix tends to be lower when compared to a short-term (1-3 h) toxicity test in pure culture media. Incorporation of 1 ng kg
−1
to 5 g kg
−1
GNMs in soil for an exposure time of 3 to 365 days showed a transient effect on the soil microbial community, their activity, and soil function. When plant productivity is considered, addition of 50 mg kg
−1
to 150 g kg
−1
GNMs into soil showed positive impacts on plant productivity for an exposure time of 3 h to 120 days. However, it is important to note that outcomes of GNM interaction in agriculture will depend significantly on factors such as the type of GNM, application dose, exposure time, and experimental conditions. Additionally, in subsurface soil, GNMs are likely to bio-transform, which will alter their biotic/abiotic interactions. The understanding of how GNMs impact agriculture is still in its infancy, and there are discrepancies in study findings primarily due to the diversity and complexity across agricultural systems. There is a need for mechanistically enriched research on GNM interaction and fate in agricultural systems that will pave the way to efficient design of GNM application in improving yield and to obtain a food secured future.
To achieve a world without hunger, it is imperative to address the inefficiencies within the current agricultural system by adopting innovative and sustainable approaches.
The fate of fertilizer nitrogen (N) in flooded agroecosystems is difficult to predict given the multitude of potential N transformation pathways. In particular, rhizosphere effects are known to play ...a significant role in N cycling, but are especially difficult to quantify in large emergent macrophytes. To address these issues, we utilized a whole core 15NH4+ perfusion technique with porewater equilibrators for the extraction of 14+15N–NO3−, NH4+, and N2. Sub-surface denitrification was found to be an important N loss pathway in wetland sediments vegetated with aerenchymatous taro (Colocasia esculenta) versus bare sediments. Driven by hypothesized thermo-osmotic mechanisms linked to photosynthesis, diurnal O2 transport into the sub-surface stimulated nitrification–denitrification in the extensive root rhizosphere. Porewater denitrification rates were also positively influenced by airflow across leaf surfaces. Depth-integrated porewater denitrification rates in this system were very high, ranging from 23 to 845 μmol N2 m−2 h−1. The N cycling functional genes nosZ and amoA were found at high abundances throughout the sub-surface with nirS dominating nitrite reduction in these sediments. Overall we were able to account for >82% of added 15NH4+ in the vegetated cores over a ten-day incubation through both plant incorporation and surface/sub-surface coupled nitrification–denitrification. In summary, these results suggested (1) that oxygen flux through the taro stem and root system into the flooded sediment may be an important driver of nitrification and coupled denitrification in these systems, and (2) that oxygen flux is mediated by air movement (wind) and the diurnal light-cycle related to photosynthesis.
►We examine the effect of emergent macrophytes on the nitrification–denitrification pathway. ► We use a modified 15NH4+ whole core perfusion technique in a flooded agricultural wetland. ► Vegetation enhances sub-surface coupled nitrification–denitrification versus control cores. ► Air movement has a large positive effect on sub-surface coupled nitrification–denitrification. ► Sub-surface N losses were more important than losses from the surface oxic/anoxic interface.
In a warmer world, microbial decomposition of previously frozen organic carbon (C) is one of the most likely positive climate feedbacks of permafrost regions to the atmosphere. However, mechanistic ...understanding of microbial mediation on chemically recalcitrant C instability is limited; thus, it is crucial to identify and evaluate active decomposers of chemically recalcitrant C, which is essential for predicting C-cycle feedbacks and their relative strength of influence on climate change. Using stable isotope probing of the active layer of Arctic tundra soils after depleting soil labile C through a 975-day laboratory incubation, the identity of microbial decomposers of lignin and, their responses to warming were revealed.
The β-Proteobacteria genus Burkholderia accounted for 95.1% of total abundance of potential lignin decomposers. Consistently, Burkholderia isolated from our tundra soils could grow with lignin as the sole C source. A 2.2 °C increase of warming considerably increased total abundance and functional capacities of all potential lignin decomposers. In addition to Burkholderia, α-Proteobacteria capable of lignin decomposition (e.g. Bradyrhizobium and Methylobacterium genera) were stimulated by warming by 82-fold. Those community changes collectively doubled the priming effect, i.e., decomposition of existing C after fresh C input to soil. Consequently, warming aggravates soil C instability, as verified by microbially enabled climate-C modeling.
Our findings are alarming, which demonstrate that accelerated C decomposition under warming conditions will make tundra soils a larger biospheric C source than anticipated. Video Abstract.
We examined the effect of different soil sample sizes obtained from an agricultural field, under a single cropping system uniform in soil properties and aboveground crop responses, on bacterial and ...fungal community structure and microbial diversity indices. DNA extracted from soil sample sizes of 0.25, 1, 5, and 10 g using MoBIO kits and from 10 and 100 g sizes using a bead-beating method (SARDI) were used as templates for high-throughput sequencing of 16S and 28S rRNA gene amplicons for bacteria and fungi, respectively, on the Illumina MiSeq and Roche 454 platforms. Sample size significantly affected overall bacterial and fungal community structure, replicate dispersion and the number of operational taxonomic units (OTUs) retrieved. Richness, evenness and diversity were also significantly affected. The largest diversity estimates were always associated with the 10 g MoBIO extractions with a corresponding reduction in replicate dispersion. For the fungal data, smaller MoBIO extractions identified more unclassified Eukaryota incertae sedis and unclassified glomeromycota while the SARDI method retrieved more abundant OTUs containing unclassified Pleosporales and the fungal genera Alternaria and Cercophora. Overall, these findings indicate that a 10 g soil DNA extraction is most suitable for both soil bacterial and fungal communities for retrieving optimal diversity while still capturing rarer taxa in concert with decreasing replicate variation.
Air carries a diverse load of particulate microscopic biological matter in suspension, either aerosolized or aggregated with dust particles, the aerobiome, which is dispersed by winds from sources to ...sinks. The aerobiome is known to contain microbes, including pathogens, as well as debris or small-sized propagules from plants and animals, but its variability and composition has not been studied comprehensibly. To gain a dynamic insight into the aerobiome existing over a mixed-use dryland setting, we conducted a biologically comprehensive, year-long survey of its composition and dynamics for particles less than 10 μm in diameter based on quantitative analyses of DNA content coupled to genomic sequencing. Airborne biological loads were more dependent on seasonal events than on meteorological conditions and only weakly correlated with dust loads. Core aerobiome species could be understood as a mixture of high elevation (e.g. Microbacteriaceae, Micrococcaceae, Deinococci), and local plant and soil sources (e.g. Sphingomonas, Streptomyces, Acinetobacter). Despite the mixed used of the land surrounding the sampling site, taxa that contributed to high load events were largely traceable to proximal agricultural practices like cotton and livestock farming. This included not only the predominance of specific crop plant signals over those of native vegetation, but also that of their pathogens (bacterial, viral and eukaryotic). Faecal bacterial loads were also seasonally important, possibly sourced in intensive animal husbandry or manure fertilization activity, and this microbial load was enriched in tetracycline resistance genes. The presence of the native opportunistic pathogen, Coccidioides spp., by contrast, was detected only with highly sensitive techniques, and only rarely. We conclude that agricultural activity exerts a much stronger influence that the native vegetation as a mass loss factor to the land system and as an input to dryland aerobiomes, including in the dispersal of plant, animal and human pathogens and their genetic resistance characteristics.
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•Airborne particles transmit eukaryotes, prokaryotes, viruses, including pathogens.•The “aerobiome” of a mixed land-use dryland ecosystem was monitored over a year.•Seasonal anthropogenic activity associated with agriculture drove aerobiome loads.•Crop harvest, animal husbandry contributed human, plant and animal pathogens.•Agriculture, not native desert, primarily shapes the aerobiome in mixed drylands.
Over the past few decades, regulatory RNAs, such as small RNAs (sRNAs), have received increasing attention in the context of host-microbe interactions due to their diverse roles in controlling ...various biological processes in eukaryotes. In addition, studies have identified an increasing number of sRNAs with novel functions across a wide range of bacteria. What is not well understood is why cells regulate gene expression through post-transcriptional mechanisms rather than at the initiation of transcription. The finding of a multitude of sRNAs and their identified associated targets has allowed further investigation into the role of sRNAs in mediating gene regulation. These foundational data allow for further development of hypotheses concerning how a precise control of gene activity is accomplished through the combination of transcriptional and post-transcriptional regulation. Recently, sRNAs have been reported to participate in interkingdom communication and signalling where sRNAs originating from one kingdom are able to target or control gene expression in another kingdom. For example, small RNAs of fungal pathogens that silence plant genes and vice-versa plant sRNAs that mediate bacterial gene expression. However, there is currently a lack of evidence regarding sRNA-based inter-kingdom signalling across more than two interacting organisms. A habitat that provides an excellent opportunity to investigate interconnectivity is the plant rhizosphere, a multifaceted ecosystem where plants and associated soil microbes are known to interact. In this paper, we discuss how the interconnectivity of bacteria, fungi, and plants within the rhizosphere may be mediated by bacterial sRNAs with a particular focus on disease suppressive and non-suppressive soils. We discuss the potential roles sRNAs may play in the below-ground world and identify potential areas of future research, particularly in reference to the regulation of plant immunity genes by bacterial and fungal communities in disease-suppressive and non-disease-suppressive soils.
The significance of anaerobic ammonium oxidation (anammox) for nitrogen removal in deep continental margin sediments was studied with ¹⁵N amendments to suboxic sediments collected from 2800–3100-m ...water depth at eight sites in the Cascadia Basin (eastern North Pacific Ocean). Consistent with earlier data from deep continental margin sediments, pore-water distributions of inorganic N indicated
$NH_4^ + $
removal from suboxic zone sediments, likely due to reaction with nitrate. Anammox rates estimated from suboxic sediment incubations with ¹⁵N-labled substrates ranged between 0.065 and 1.7 nmol N mL⁻¹ h⁻¹ (wet sediment), which suggested that anammox was responsible for the observed
$NH_4^ + $
removal. Anammox and denitrification rates derived from
$NH_3^ - $
and
$NH_4^ + $
pore-water profiles were 32- 82 µ mol N m⁻² d⁻¹ and 50-110 µmol N m⁻² d⁻¹, respectively. The average contribution of anammox to total N₂ production was 40% (¹⁵N-amended sediment incubations) to 42% (flux from pore-water inorganic N), which does not support earlier reports that suggested that the relative importance of anammox increased with water depth and thereby should dominate over denitrification at depths greater than 1000 m.
Denitrification is an important global N cycle process. The gene encoding NosZ that converts nitrous oxide (N
2
O) to N
2
has been widely used as a biomarker to study denitrifying communities. ...However, conventional PCR primers target a limited range of the genetically diverse Clade I
nosZ
, and the amplicons are too long for sequencing on current NGS platforms. To address these issues, we developed a new PCR primer set that amplifies a 355-bp region of Clade I
nosZ
and captures broader taxonomic coverage than conventional primers in in silico tests. When compared with the widely used nosZF_nosZR_Rich_2003 set using the same soil samples and the same sequencing depth, the new set retrieved genes from four times more unique species, with consistently higher general diversity-based metrics. The new primer set performed well with different sequencing platforms (Ion Torrent and Illumina), and among a wide variety of soils from polar to tropical, desert to agricultural, and surface to a very low biomass subsoil, with significant differences in denitrifying community diversity and composition. This new primer set for Clade I together with the primers recently reported for Clade II by Chee-Sanford et al. (
J Microbiol Meth
172:105908,
2020
) provides a more comprehensive assessment of denitrifier gene hosts, their ecological patterns, and the degree of novelty in retrieved gene sequences.
Eutrophication caused by anthropogenic nutrient inputs is one of the greatest threats to the integrity of freshwater wetlands. The resultant changes in organic carbon cycling and nutrient ...mineralization may be expressed through increased decomposition rates, which are ultimately dependent on the metabolism of the resident microbial community. Specifically, microbial nutrient acquisition is controlled through the activity of enzymes, which are in turn influenced by local biogeochemical conditions. This study examines enzyme activities along distinct North-South P gradients within four distinct hydrologic units of the Florida Everglades. The results indicate that nutrient enriched sites exhibit lower N and P limitations on microbially constrained C mineralization, in addition to enhanced cellulose decomposition rates. Nutrient loading resulted in decreased microbial mobilization of resources for P mineralization, resulting in greater energetic allocation for C mineralization. Additionally, N appears to become less limiting to C mineralization in the enriched sites within Everglades National Park, the least P enriched area within the Everglades. A simple two component model, incorporating total P and the relationship between the enzymes involved in C and P mineralization accounted for between 46 and 92% of the variability in measured cellulose decomposition rates and thus demonstrates the significant influence that P loading plays in these systems. These results also suggest there is an environmental threshold TP concentration below which changes in enzyme-based resource allocation will not occur.
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