Nitrogen-fixing bacterial communities differ between perennial agroecosystem crops

Biocrusts, common in natural ecosystems, are specific assemblages of microorganisms at or on the soil surface with associated microorganisms extending into the top centimeter of soil. Agroecosystem biocrusts have similar rates of nitrogen (N) fixation as those in natural ecosystems, but it is unclear how agricultural management influences their composition and function. This study examined the total bacterial and diazotrophic communities of biocrusts in a citrus orchard and a vineyard that shared similar climate and soil type but differed in management. To contrast climate and soil type, these biocrusts were also compared to those from an apple orchard. Unlike natural ecosystem biocrusts, these agroecosystem biocrusts were dominated by proteobacteria and had a lower abundance of cyanobacteria. All examined agroecosystem biocrust diazotroph communities were dominated by N-fixing cyanobacteria from the Nostocales order, similar to natural ecosystem cyanobacterial biocrusts. Lower irrigation and fertilizer in the vineyard compared to the citrus orchard could have contributed to biocrust microbial composition, whereas soil type and climate could have differentiated the apple orchard biocrust. Season did not influence bacterial and diazotrophic community composition of any these agroecosystem biocrusts. Overall, agricultural management and climatic and edaphic factors potentially influenced community composition and function of these biocrusts.

Impact of repeated fumigant applications on soil properties, crop yield, and microbial communities in a plastic-mulched tomato production system

Pre-plant soil fumigation is widely applied to control nematodes, soil-borne fungal pathogens, and weeds in vegetable crops. However, most of the research evaluating the effect of fumigants on crop yield and soil microbial communities has been done on single compounds despite growers mainly applying fumigant combinations. We studied the effect of different fumigant combinations (chloropicrin, 1,3-dichloropropene, and metam potassium) on soil properties, crop yield, and the soil bacterial and fungal microbiome for two consecutive years in a plastic-mulched tomato production system in Florida (United States). While combinations of fumigants did not improve plant productivity more than the individual application of these products, application of fumigants with >60 % chloropicrin did significantly increase yield. Fumigant combinations had no significant effect on bacterial diversity, but fumigants with >35 % chloropicrin reduced soil fungal diversity and induced temporary changes in the soil bacterial and fungal community composition. These changes included short-term increases in the relative abundance of Firmicutes and Ascomycota, as well as decreases in other bacterial and fungal taxa. Repeated fumigation reduced network complexity and the relative abundance of several predicted bacterial functions and fungal guilds, particularly after fumigation and at end of harvest (3-months post fumigation). A structural equation model (SEM) showed fumigants not only directly impact crop yield, but they can also indirectly determine variations in plant productivity through effects on the soil microbiome. Overall, this study increases our understanding of the environmental and agricultural impacts of fumigants in a plastic-mulched tomato production system.

Interactions between rootstocks and compost influence the active rhizosphere bacterial communities in citrus

BACKGROUND

While the rootstock genotype (belowground part of a plant) can impact rhizosphere microbial communities, few studies have examined the relationships between rootstock genotype-based recruitment of active rhizosphere bacterial communities and the availability of root nutrients for plant uptake. Rootstocks are developed to provide resistance to disease or tolerance of abiotic stresses, and compost application is a common practice to also control biotic and abiotic stresses in crops. In this field study, we examined: (i) the effect of four citrus rootstocks and/or compost application on the abundance, diversity, composition, and predicted functionality of active rhizosphere bacterial communities, and (ii) the relationships between active rhizosphere bacterial communities and root nutrient concentrations, with identification of bacterial taxa significantly correlated with changes in root nutrients in the rhizosphere.

RESULTS

The rootstock genotype determined differences in the diversity of active rhizosphere bacterial communities and also impacted how compost altered the abundance, diversity, composition, and predicted functions of these active communities. Variations in the active bacterial rhizobiome were strongly linked to root nutrient cycling, and these interactions were root-nutrient- and rootstock-specific. Direct positive relationships between enriched taxa in treated soils and specific root nutrients were detected, and potentially important taxa for root nutrient uptake were identified. Significant differences in specific predicted functions were related to soil nutrient cycling (carbon, nitrogen, and tryptophan metabolisms) in the active bacterial rhizobiome among rootstocks, particularly in soils treated with compost.

CONCLUSIONS

This study illustrates that interactions between citrus rootstocks and compost can influence active rhizosphere bacterial communities, which impact root nutrient concentrations. In particular, the response of the rhizobiome bacterial abundance, diversity, and community composition to compost was determined by the rootstock. Specific bacterial taxa therefore appear to be driving changes in root nutrient concentrations in the active rhizobiome of different citrus rootstocks. Several potential functions of active bacterial rhizobiomes recruited by different citrus rootstocks did not appear to be redundant but rather rootstock-specific. Together, these findings have important agronomic implications as they indicate the potential for agricultural production systems to maximize benefits from rhizobiomes through the choice of selected rootstocks and the application of compost. Video Abstract.

Effect of fumigants and non-fumigants on nematode and weed control, crop yield, and soil microbial diversity and predicted functionality in a strawberry production system

Fumigants are commonly used to control soil-borne pathogens of high-value crops, but they may also impact non-target soil microorganisms. Increasing interest in the use of sustainable management practices to control plant- and root-parasitic nematodes has resulted in the formulation of non-fumigant nematicides (chemicals or bionematicides) which are considered environmentally friendly alternatives to fumigants. However, the impact of these new products compared to standard fumigants on soil-borne pathogens, plant production, and the diversity and composition of non-target microbial communities in all crops remains unclear. To begin to address this knowledge gap, we examined the effect of fumigants commonly used in Florida (United States) strawberry production and newly formulated non-fumigant nematicides on nematode and weed control, plant growth, crop yield, and bacterial and fungal community diversity and predicted functionality. We found the standard fumigants increased crop yields and reduced weed pressure more than non-fumigants. Both fumigants and non-fumigants were an efficient management strategy to control sting nematodes. Treatments also impacted the abundance of specific beneficial and antagonistic taxa. Both fumigants and non-fumigants reduced soil bacterial and fungal diversity, an effect that remained for six months, thus suggesting a potential residual impact of these products on soil microorganisms. However, only fumigants altered soil microbial community composition and reduced network complexity, inducing a decrease or even a loss of some predicted bacterial and fungal functions, particularly during the first weeks after fumigation. Nevertheless, soil collected at the end of the season showed significant levels of root-knot nematode suppression in a growth chamber experiment, irrespective of the previous treatment. By linking the effect of fumigants and non-fumigants on soil-borne pests, plant and production, and the soil microbiome, this study increases our knowledge regarding the environmental impact of these products.

Native Rhizobia Improve Plant Growth, Fix N2, and Reduce Greenhouse Emissions of Sunnhemp More than Commercial Rhizobia Inoculants in Florida Citrus Orchards

Sunnhemp (Crotalaria juncea L.) is an important legume cover crop used in tree cropping systems, where there is increased interest by growers to identify rhizobia to maximize soil nitrogen (N) inputs. We aimed to isolate and identify native rhizobia and compare their capabilities with non-native rhizobia from commercial inoculants to fix atmospheric dinitrogen (N₂), produce and reduce nitrous oxide (N₂O), and improve plant growth. Phylogenetic analyses of sequences of the 16S rRNA and recA, atpD, and glnII genes showed native rhizobial strains belonged to Rhizobium tropici and the non-native strain to Bradyrhizobium japonicum. Plant nodulation tests, sequencing of nodC and nifH genes, and the acetylene-dependent ethylene production assay confirmed the capacity of all strains to nodulate sunnhemp and fix N₂. Inoculation with native rhizobial strains resulted in significant increases in root and shoot weight and total C and N contents in the shoots, and showed greater N₂-fixation rates and lower emissions of N₂O compared to the non-native rhizobium. Our results suggest that native rhizobia improve plant growth, fix N₂, and reduce greenhouse emissions of sunnhemp more than commercial rhizobia inoculants in Florida citrus orchards.

Contrasting seasonal patterns and factors regulating biocrust N2-fixation in two Florida agroecosystems

Biocrusts are communities of microorganisms within the top centimeter of soil, often dominated by phototrophic dinitrogen-fixing (N₂-fixing) organisms. They are common globally in arid ecosystems and have recently been identified in agroecosystems. However, unlike natural ecosystem biocrusts, agroecosystem biocrusts receive regular fertilizer and irrigation inputs. These inputs could influence seasonal biocrust N₂-fixation and their relationship with soil nutrients in perennial agroecosystems, which is of particular interest given crop management requirements. In this study, biocrust and adjacent bare soil N₂-fixation activity was measured in the field during the summer, fall, spring, and winter seasons in a Florida citrus orchard and vineyard using both acetylene reduction assays and ¹⁵N₂ incubations. Samples were analyzed for microbial and extractable carbon (MBC, EC), nitrogen (MBN, EN), and phosphorus (MBP, EP). In both agroecosystems, biocrusts had greater microbial biomass and extractable nutrients compared to bare soil. The citrus and grape biocrusts were both actively fixing N₂, despite crop fertilization, with rates similar to those found in natural arid and mesic systems, from 0.1 to 142 nmol of C₂H₄ g^–1 of biocrust dry weight h^–1 (equivalent to 1–401 μmol m^–2h^–1). Lower soil temperatures and higher EC:EN ratios were associated with higher N₂-fixation rates in citrus biocrusts, while higher soil moisture and higher EP were associated with higher N₂-fixation rates in grape biocrusts. The N₂-fixation activity of these agroecosystem biocrusts indicates the possibility of biocrusts to enhance N cycling in perennial agroecosystems, with potential benefits for crop production.

Impact of fumigants on non-target soil microorganisms: a review

Fumigants have been used for decades to control soil-borne pathogens of high-value crops, and increasing evidence indicates they can affect non-target soil microbial communities. Understanding the impacts of these products on soil microorganisms is of critical importance not only for evaluating their environmental safety, but also because soil microbial communities have a central role in soil quality and nutrient cycling, plant growth, and crop production. Thus, we conducted a systematic review and metanalysis study of fumigant impacts on non-target soil microorganisms. In general, we found that fumigation decreases the bacterial diversity and abundance of total bacteria and nitrogen-cycling genes by approximately 10-50% during the first four weeks after application compared to non-treated soils. These decreases appear transient and tend to diminish or disappear after four weeks. Increases in bacterial diversity and abundance can occur after fumigation but are less common. Fumigant application can also alter bacterial community composition during the first six weeks after treatment by significantly increasing and/or decreasing the relative abundance of bacterial taxa involved in key soil functions such as N-cycling and plant-growth promotion. Knowledge gaps and areas where future research efforts should be prioritized to improve our understanding of the impact of organic fumigants on non-target soil microorganisms are discussed.

Impact of Soil Microbial Amendments on Tomato Rhizosphere Microbiome and Plant Growth in Field Soil

There is increased interest by the agricultural industry in microbial amendments that leverage natural beneficial interactions between plants and soil microbes to improve crop production. However, translating fundamental knowledge from laboratory experiments into efficient field application often has mixed results, and there is less clarity about the interaction between added microbes and the native microbial community, where microorganisms belonging to the same phylogenic clades often reside. In this study, four commercially available microbial amendments were examined in two greenhouse experiments using field soil to assess their impact on tomato plant growth and the native soil microbial communities. The amendments contained different formulations of plant growth-promoting bacteria (Lactobacilli, Rhizobia, etc.), yeasts, and mycorrhizal fungi. The application of the tested amendments in greenhouse conditions resulted in no significant impact on plant growth. A deeper statistical analysis detected variations in the microbial communities that accounted only for 0.25% of the total species, particularly in native taxa not related to the inoculated species and represented less than 1% of the total variance. This suggests that under commercial field conditions, additional confounding variables may play a role in the efficacy of soil microbial amendments. This study confirms the necessity of more in-depth validation requirements for the formulations of soil microbial amendments before delivery to the agricultural market in order to leverage their benefits for the producers, the consumers, and the environment.

Impact of Cover Crops on the Soil Microbiome of Tree Crops

Increased concerns associated with interactions between herbicides, inorganic fertilizers, soil nutrient availability, and plant phytotoxicity in perennial tree crop production systems have renewed interest in the use of cover crops in the inter-row middles or between trees as an alternative sustainable management strategy for these systems. Although interactions between the soil microbiome and cover crops have been examined for annual cropping systems, there are critical differences in management and growth in perennial cropping systems that can influence the soil microbiome and, therefore, the response to cover crops. Here, we discuss the importance of cover crops in tree cropping systems using multispecies cover crop mixtures and minimum tillage and no-tillage to not only enhance the soil microbiome but also carbon, nitrogen, and phosphorus cycling compared to monocropping, conventional tillage, and inorganic fertilization. We also identify potentially important taxa and research gaps that need to be addressed to facilitate assessments of the relationships between cover crops, soil microbes, and the health of tree crops. Additional evaluations of the interactions between the soil microbiome, cover crops, nutrient cycling, and tree performance will allow for more effective and sustainable management of perennial cropping systems.

Brassica seed meal soil amendments transform the rhizosphere microbiome and improve apple production through resistance to pathogen reinfestation

Brassicaceae seed meal (SM) formulations were compared with preplant 1,3-dichloropropene/chloropicrin (Telone-C17) soil fumigation for the ability to control apple replant disease and to suppress pathogen or parasite reinfestation of organic orchard soils at two sites in Washington State. Preplant soil fumigation and an SM formulation consisting of either Brassica juncea-Sinapis alba or B. juncea-B. napus each provided similar levels of disease control during the initial growing season. Although tree growth was similar in fumigated and SM-amended soil during the initial growing season, tree performance in terms of growth and yield was commonly superior in B. juncea-S. alba SM-amended soil relative to that in fumigated soil at the end of four growing seasons. SM-amended soils were resistant to reinfestation by Pratylenchus penetrans and Pythium spp. relative to fumigated soils and corresponded with enhanced tree performance. Phytotoxic symptoms were observed in response to SM amendment at one of two orchard sites, were dependent upon season of application, and occurred in an SM formulation-specific manner. After 2 years, the rhizosphere microbiome in fumigated soils had reverted to one that was indistinguishable from the no-treatment control. In contrast, rhizosphere soils from the SM treatment possessed unique bacterial and fungal profiles, including specific microbial elements previously associated with suppression of plant-pathogenic fungi, oomycetes, and nematodes. Overall diversity of the microbiome was reduced in the SM treatment rhizosphere, suggesting that enhanced "biodiversity" was not instrumental in achieving system resistance or pathogen suppression.

Hypochlorite-modified adenine nucleotides: structure, spin-trapping, and formation by activated guinea pig polymorphonuclear leukocytes

Adenosine and its nucleotides react with hypochlorite to form unstable products that have been identified as the N6 chloramine derivatives. These chloramines spontaneously oligomerize, form stable adducts with proteins and nucleic acids, and are converted with loss of chlorine to the original nucleoside or nucleotide by reducing agents. The chloramines are associated with a free radical, and the spin-trapping of adenosine chloramine with 5,5-dimethyl-1-pyrroline-N-oxide (DMPO) yielded a mixture of unstable nitroxyl adducts that corresponded to nitrogen-centered radicals from the parent nucleoside. When activated guinea pig polymorphonuclear leukocytes were stimulated with phorbol myristate acetate to produce hypochlorite, they actively incorporated [14C]adenosine into acid-insoluble products by a process that was dependent on oxygen and inhibited by azide and thiols. These findings suggest that adenine nucleotide chloramines are generated by activated phagocytic cells and form ligands with proteins and nucleic acids as observed in model systems. The results imply that nucleotide chloramines are among the cytotoxic and possibly mutagenic factors that are associated with the inflammatory process.

Carrier-mediated transport of enkephalins and N-Tyr-MIF-1 across blood-brain barrier

The saturable, carrier-mediated system capable of the brain-to-blood transport of small peptides with an N-terminal tyrosine was characterized. The rate of disappearance of intraventricularly injected iodinated peptide in the presence or absence of the inhibitor being tested was determined from formulas based on the residual radioactivity in the brains of mice after decapitation. The injection of 100 nmol/mouse of unlabeled N-Tyr-MIF-1 (TMIF) increased the half-time disappearance of 125I-TMIF (ITMIF) in the central nervous system (CNS) from 14.1 to 88.7 min (P less than 0.00005). Technetium, a substance transported out of the brain by the same system that transports iodine, was used as a control; the half-time disappearance of technetium pertechnetate was unaffected by unlabeled TMIF. With two related but distinct techniques, the maximum transport rate out of the CNS (Vmax) for TMIF was 0.266 nmol X g of brain per min (method 1) and 0.297 nmol X g-1 X min-1 (method 2), while the amount of unlabeled material needed to achieve 50% of Vmax (Km) was 15.2 nmol/g (method 1) and 15.1 nmol/g (method 2). The lack of effect of the tyrosinated fragments of TMIF as inhibitors indicates that TMIF is being transported in intact form. The Vmax for methionine enkephalin determined with labeled and unlabeled methionine enkephalin was 0.630 nmol X g-1 X min-1 and the Km was 24.95 nmol/g. Studies with the metabolic modulators furosemide, acetozolamide, reserpine, ouabain, and theophylline suggest that the system is sodium dependent and probably independent of ATPase.(ABSTRACT TRUNCATED AT 250 WORDS)