Since nitrogen (N) is often limiting in permafrost soils, we investigated the N
-fixing genetic potential and the inferred taxa harboring those genes by sequencing
gene fragments in samples taken ...along a permafrost thaw gradient in an Alaskan boreal soil. Samples from minimally, moderately and extensively thawed sites were taken to a depth of 79 cm to encompass zones above and below the depth of the water table.
reads were translated with frameshift correction and 112,476 sequences were clustered at 5% amino acid dissimilarity resulting in 1,631 OTUs. Sample depth in relation to water table depth was correlated to differences in the
sequence classes with those most closely related to group I
-harboring Alpha- and Beta-Proteobacteria in higher abundance above water table depth while those related to group III
-harboring Delta Proteobacteria more abundant below. The most dominant below water table depth
sequences, comprising 1/3 of the total, were distantly related to
-
. Overall, these results suggest that permafrost thaw alters the class-level composition of N
-fixing communities in the thawed soil layers and that this distinction corresponds to the depth of the water table. These
data were also compared to
sequences obtained from a study at an Alaskan taiga site, and to those of other geographically distant, non-permafrost sites. The two Alaska sites were differentiated largely by changes in relative abundances of the same OTUs, whereas the non-Alaska sites were differentiated by the lack of many Alaskan OTUs, and the presence of unique halophilic, sulfate- and iron-reducing taxa in the Alaska sites.
The capacity for soils to perform vital functions, such as agricultural production, is dependent on numerous properties. Their simultaneous effect on soil biota is of interest to assess impacts of ...agricultural management. Using a soil quality index (SQI) based on a priori assumptions of eight soil physico-chemical properties that promote plant growth and microbial biomass, we sought to: 1) investigate the effect of land use on SQI; and 2) test a relationship between SQI and the composition of microbial functional genes. In 29 soils under four distinct land uses (cotton, wheat, pasture and native vegetation) gene composition was most distinct in cotton. The SQI followed the gradient cotton < wheat < native vegetation < pasture, with pasture significantly greater than other land uses. Of 67 functional gene markers, gradient boosted machine learning identified five genes that correlated strongly with SQI. These were stress response (oxyR and dnaJ), core carbon, nitrogen and sulfur metabolism (PTS-Glc-EIIA, glnH and sat, respectively). Nutrient cycling functional genes did not correlate with SQI. A structural equation model of the relationship between soil properties, SQI, and the aforementioned genes was used to visualise these interactions (root mean squared error of 0.1, R2 of 0.64 and p < 0.001). We conclude that certain land use practices improve or degrade soil quality relative to native vegetation, and SQI primarily correlates with microbial stress response and core metabolism. This demonstrates capacity for microbial communities to adapt to environmental stress while certain functions remain relatively resilient.
•We compared 29 soils based on a quality index derived for optimal plant growth.•The gradient followed cotton < wheat < native vegetation < pasture.•Stress response, mineral N, P, S, Fe and C cycling genes were most abundant in cotton.•Gradient boosted machine learning identified genes correlated with soil quality.•Stress response and core metabolism genes were most affected by soil quality.
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.
Enhancement of soil fertility and mitigation of atmospheric greenhouse gases are potential benefits of biochar amendments with proximate links to microbiological processes, yet the impact of biochar ...on the soil microbial community is poorly resolved. Here, we assessed changes in bacterial community composition and microbial assemblage patterns with biochar amendment in two soils with contrasting fertility under two cropping systems; perennial grass and annual sweet corn rotation at two time periods. Overall, soil type exerted the greatest effect on the soil microbial community, followed by sampling time and cropping system which exerted a greater effect on the microbial community than biochar treatment. The influence of biochar on community composition was most pronounced in the highly weathered, low fertility Oxisol, than the high fertility Mollisol. We further investigated microbial assemblage architecture using random-matrix theory based molecular ecological network analyses. Microbial assemblage complexity increased with biochar amendment, with the largest impact associated with the Oxisol, accompanied by more negative OTU co-variations, indicating enhanced competition and/or niche partitioning in concert with an increase in the number of putative “keystone species”. Network analysis suggests that biochar addition, especially in the highly weathered, low fertility Oxisol, confers higher-level organization, competition, and complexity to the soil microbiome that may result in higher resistance to change due to environmental perturbation and thereby increase system sustainability.
•The influence of biochar amendment on the soil community is dependent on soil type.•Soil bacterial communities are most responsive to biochar in Oxisol soils.•Biochar increases complexity of microbial networks in Oxisol soils.•Biochar increases microbial community resistance to environmental perturbations.
Fusarium wilt disease of banana, caused by the fungus Fusarium oxysporum f. sp. cubense race 4, is a serious soil-borne fungal disease that currently threatens worldwide banana production. No single ...agricultural practice has yet been developed to effectively manage this disease. In the present study, greenhouse experiments were conducted to evaluate the effect of an integrated biofertilizer application after ammonia fumigation to enhance control of Fusarium wilt disease in severely infected banana mono-cropped soils. Quantitative PCR and high-throughput sequencing were used to characterise soil microbial community structure and the results from both two-season experimental studies showed that biofertilizer application after ammonia fumigation significantly reduced the incidence of banana Panama disease by approximately 55% and promoted the plant biomass, compared to the control application of cow manure to non-fumigated soil. Ammonia fumigation significantly reduced total fungal and F. oxysporum abundances and bacterial and fungal diversities. Biofertilizer application after fumigation further depleted the abundance of the pathogen. Biofertilizer application and fumigation altered the soil microbial community composition with the bacterial community responding first to fumigation, while the fungal community responded first to fertilization. Although Bacillus, including our inoculated strain, was not enriched after biofertilization, putative beneficial microbes such as Paenibacillus, Virgibacillus, Nitrosomonas, and Nitrobacter, were significantly enriched by ammonia fumigation and biofertilizer application, and were significantly correlated with disease suppression or increased plant biomass. Furthermore, fumigation and biofertilization significantly increased the soil pH and nutrient contents, with concomitant effects on the microbial community. Overall, the observed disease suppression and increased plant biomass resulting from both soil fumigation and biofertilization after banana cropping can be attributed to the reduced abundance of F. oxysporum and general suppression from altered soil properties that may enable the establishment of a beneficial soil microbiome.
•Integrated biofertilizer application and fumigation enhanced Fusarium wilt disease suppression.•Ammonia fumigation significantly reduced F. oxysporum abundance.•Biofertilizer application after fumigation further depleted the abundance of the pathogen.•An increase in the number of known beneficial microbes is correlated with disease suppression.
Enzyme catalyzed reactions are generally considered the rate-limiting step in organic matter degradation and may be significantly influenced by the structure and composition of plant communities. ...Changes in these rates have the potential to effect long-term peat accumulation and influence the topography of a wetland ecosystem. To determine habitat influences on enzyme activities, we examined slough and sawgrass plots within enriched and reference phosphorus (P) sites in the Everglades. Assays were performed for the enzymes involved in carbon (C), nitrogen (N), and P cycling and lignin depolymerization. Enzyme activities were normalized and analyzed in terms of a resource allocation strategy. Plant composition was found to significantly alter the allocation of enzymatic resources due to varying substrate complexities. Potential decomposition in the slough was less influenced by lignin than in the sawgrass habitats. Additionally, an index relating hydrolytic and oxidative enzymes was significantly greater in the slough habitats, whereas C/N ratios were significantly lower. These indices suggest more favorable decomposition conditions and thus slower peat accretion within the slough communities, which may contribute to the development of elevation differences within the sawgrass ridge and slough topography of the Everglades.
Atmospheric nitrous oxide (N
O) is a potent greenhouse gas thought to be mainly derived from microbial metabolism as part of the denitrification pathway. Here we report that in unexplored peat soils ...of Central and South America, N
O production can be driven by abiotic reactions (≤98%) highly competitive to their enzymatic counterparts. Extracted soil iron positively correlated with in situ abiotic N
O production determined by isotopic tracers. Moreover, we found that microbial N
O reduction accompanied abiotic production, essentially closing a coupled abiotic-biotic N
O cycle. Anaerobic N
O consumption occurred ubiquitously (pH 6.4-3.7), with proportions of diverse clade II N
O reducers increasing with consumption rates. Our findings show that denitrification in tropical peat soils is not a purely biological process but rather a 'mosaic' of abiotic and biotic reduction reactions. We predict that hydrological and temperature fluctuations differentially affect abiotic and biotic drivers and further contribute to the high N
O flux variation in the region.
Characterizing the rhizosphere microbial community composition associated with enhanced crop yield is an important first step towards understanding the role of the microbiota in soil fertility. In ...the present study, we conducted a two-seasons field experiment in a maize-cabbage cropping system under chemical (CF), organic (OF) and bio-organic (BOF) fertilizer regimes as a model to investigate the combinatory effect of fertilizer treatment and crop type on rhizosphere soil microbiota by targeted sequencing of both the bacterial and fungal communities. The two-seasons sustainable application of bio-organic fertilizer (BOF) containing Trichoderma effectively increased maize and cabbage yields, whereas organic fertilizer (OF) increased but not significant, compared to the application of chemical fertilizer (CF). Both fertilizer treatment and crop type induced a significant effect on soil physiochemical properties and were the major factors that impacted the composition of the rhizosphere soil microbiome. Relative abundances of Trichoderma were significantly enhanced in the BOF treatment, compared to the OF and CF treatments, and exhibited significant positive relationships with crop yield improvement. The application of bio-organic fertilizer may enhance the growth promotion effect of Trichoderma and increase the abundance of potentially beneficial microbial groups such as the genera Cladorrhinum and Massilia, which were found to be highly correlated to increased crop yields. Overall, the influence of bio-organic fertilizer on crop yield is proposed to be through mechanisms by introduction of the target strain NJAU 4742 and stimulation of a potentially beneficial microbial consortia, in combination with alterations in fungal and bacterial composition and abundance, leading to an enhancement in crop yield.
•Bio-organic fertilizer containing Trichoderma increased maize and cabbage yields.•Crop type and fertilizer treatment were the major factors influenced rhizosphere microbiome.•Organic amendments affected the microbial alpha and beta diversities.•Trichoderma played an important role in crop yield enhancement.•Potentially induced beneficial microbial groups are associated with increased yields.
We analyzed the microbial community that developed after 4 years of testing different soil-crop management systems in the savannah–forest transition zone of Eastern Ghana where management systems can ...rapidly alter stored soil carbon as well as soil fertility. The agricultural managements were: (i) the local practice of fallow regrowth of native elephant grass (Pennisetum purpureum) followed by biomass burning before planting maize in the spring, (ii) the same practice but without burning and the maize receiving mineral nitrogen fertilizer, (iii) a winter crop of a legume, pigeon pea (Cajanus cajan), followed by maize, (iv) vegetation free winter period (bare fallow) followed by maize, and (v) unmanaged elephant grass-shrub vegetation. The mean soil organic carbon (SOC) contents of the soils after 4 years were: 1.29, 1.67, 1.54, 0.80 and 1.34%, respectively, differences that should affect resources for the microbial community.
From about 290,000 sequences obtained by pyrosequencing the SSU rRNA gene, canonical correspondence analysis showed that SOC was the most important factor that explained differences in microbial community structure among treatments. This analysis as well as phylogenetic ecological network construction indicated that members of the Acidobacteria GP4 and GP6 were more abundant in soils with relatively high SOC whereas Acidobacteria GP1, GP7, and Actinobacteria were more prevalent in soil with lower SOC. Burning of winter fallow vegetation led to an increase in Bacillales, especially those belonging to spore-forming genera. Of the managements, pigeon-pea cultivation during the winter period promoted a higher microbial diversity and also sequestered more SOC, presumably improving soil structure, fertility, and resiliency.
•50% loss of SOC and biomass in 4 years reshapes the tropical microbial community.•But, soil microbial community structure is remarkably resilient to resource loss.•Acidobacteria groups are most responsive to SOC changes.•Plant residue burning increased the abundance of Bacillales.•N2-fixing fallow crop increased microbial diversity and improved soil fertility.
Graphene nanofertilizers have demonstrated immense potential in improving agricultural productivity and nitrogen management. However, how those nanomaterials interact with soil microbial communities ...related to N cycle remain unclear. The present study assessed the impact of four different graphitic nanomaterials (i.e., GO, graphene oxide; rGO, reduced graphene oxide; GNP, graphene nanoplatelet; GNA, graphite nanoadditive) and biochar at two different doses (5 and 1000 mg kg
−1
soil) on soil respiration, nitrification potential, and microbial N cycling functional genes over 28 days of incubation of sandy agricultural soil. Basal respiration indicated a transient increase of microbial activity with all treatments, while substrate induced respiration (SIR) revealed an enhancement of microbial respiration rate with some treatments that sustained at the end of the incubation. No significant differences in the maximum nitrification potential were observed when treated with GNMs or biochar. However, decreased abundances of
amoA
genes and increased abundance of denitrifying genes (
nirK
,
nirS
,
nosZ
) in all treated soils suggested a decreased potential for nitrification and boosted denitrification after 28-day exposure. In addition, GNMs showed minimum impact on
nifH
population in this incubation study. Together, the results suggest that graphitic nanomaterials might suppress nitrification and potentially reduce losses by nitrate leaching in agricultural soils.
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