Shifts in Soil Bacterial Communities as a Function of Carbon Source Used During Anaerobic Soil Disinfestation

Anaerobic soil disinfestation (ASD) is an organic amendment-based management practice for controlling soil-borne plant pathogens. Pathogen suppression appears to be carbon source-dependent and mediated by bacteria that proliferate and produce volatile organic compounds, as well as physico-chemical changes (i.e., elevated temperature, lowered redox potential and pH, release of metal ions) in soil. ASD is under study for adoption in tree crops as a replacement for chemical-fumigation, but its widespread use is limited by incomplete understanding of its suppression mechanisms and high economic costs. The carbon substrate is one component of the ASD process that can be optimized to enhance effectiveness and affordability. While rice bran is currently the standard carbon source used for ASD, we identified three alternative substrates (molasses, mustard seed meal, and tomato pomace) that are similar in efficacy to rice bran at generating and sustaining soil anoxia and reducing populations of introduced plant pathogens. Here, we used replicated ASD field trials to determine if rice bran and the alternative carbon substrates would elicit similar soil bacterial communities (characterized via amplicon sequencing of the 16S rRNA gene v4 region) and to assess if any observed community shifts were consistent across repeated trials. We found significant, but minimal differences in community composition between ASD carbon treatments (F4, 30 = 2.80, P < 0.001, R2 = 0.22) and trials (F1, 30 = 5.24, P < 0.001, R2 = 0.10). In both trials, the abundances of Bacteroidales, Clostridiales, Selenomonadales, and Enterobacteriales increased significantly (>5 log2 fold change) in all ASD treatments compared to untreated controls. A group of shared core genera belonging to the Clostridiales and Selenomonadales were identified in both trials and constituted 22.6 and 21.5% of the communities. Bacterial taxa that were most responsive to ASD treatments had the genomic potential for denitrification, nitrogen fixation, and fermentation reactions that produce organic acids (such as acetate and butyrate) known to inhibit in vitro growth of plant pathogens based on predicted metagenomes. Together, these results indicate that reproducible and effective implementation of ASD is achievable with alternative carbon substrates to rice bran

Coping with iron limitation : a metabolomic study of Synechocystis sp. PCC 6803

Iron (Fe) is a key element for all living systems, especially for photosynthetic organisms because of its important role in the photosynthetic electron transport chain. Fe limitation in cyanobacteria leads to several physiological and morphological changes. However, the overall metabolic responses to Fe limitation are still poorly understood. In this study, we integrated elemental, stoichiometric, macromolecular, and metabolomic data to shed light on the responses of Synechocystis sp. PCC 6803, a non-N2-fixing freshwater cyanobacterium, to Fe limitation. Compared to Synechocystis growing at nutrient replete conditions, Fe-limited cultures had lower growth rates and amounts of chlorophyll a, RNA, RNA:DNA, C, N, and P, and higher ratios of protein:RNA, C:N, C:P, and N:P, in accordance with the growth rate hypothesis which predicts faster growing organisms will have decreased biomass RNA contents and C:P and N:P ratios. Fe-limited Synechocystis had lower amounts Fe, Mn, and Mo, and higher amount of Cu. Several changes in amino acids of cultures growing under Fe limitation suggest nitrogen limitation. In addition, we found substantial increases in stress-related metabolites in Fe-limited cyanobacteria such antioxidants. This study represents an advance in understanding the stoichiometric, macromolecular, and metabolic strategies that cyanobacteria use to cope with Fe limitation. This information, moreover, may further understanding of changes in cyanobacterial functions under scenarios of Fe limitation in aquatic ecosystems

Characterization of Two New Genes, amoR and amoD, in the amo Operon of the Marine Ammonia Oxidizer Nitrosococcus oceani ATCC 19707

Molecular analysis of the amo gene cluster in Nitrosococcus oceani revealed that it consists of five genes, instead of the three known genes, amoCAB . The two additional genes, orf1 and orf5 , were introduced as amoR and amoD , respectively. Putative functions of the AmoR and AmoD proteins are discussed

Has agricultural intensification impacted maize root traits and rhizosphere interactions related to organic N acquisition?

Plant-microbe interactions in the rhizosphere influence rates of organic matter mineralization and nutrient cycling that are critical to sustainable agricultural productivity. Agricultural intensification, particularly the introduction of synthetic fertilizer in the USA, altered the abundance and dominant forms of nitrogen (N), a critical plant nutrient, potentially imposing selection pressure on plant traits and plant-microbe interactions regulating N cycling and acquisition. We hypothesized that maize adaptation to synthetic N fertilization altered root functional traits and rhizosphere microbial nutrient cycling, reducing maize ability to acquire N from organic sources. Six maize genotypes released pre-fertilizer (1936, 1939, 1942) or post-fertilizer (1984, 1994, 2015) were grown in rhizoboxes containing patches of 15N-labelled clover/vetch residue. Multivariate approaches did not identify architectural traits that strongly and consistently predicted rhizosphere processes, though metrics of root morphological plasticity were linked to carbon- and N-cycling enzyme activities. Root traits, potential activities of extracellular enzymes (BG, LAP, NAG, urease), abundances of N-cycling genes (amoA, narG, nirK, nirS, nosZ) and uptake of organic N did not differ between eras of release despite substantial variation among genotypes and replicates. Thus, agricultural intensification does not appear to have impaired N cycling and acquisition from organic sources by modern maize and its rhizobiome. Improved mechanistic understanding of rhizosphere processes and their response to selective pressures will contribute greatly to rhizosphere engineering for sustainable agriculture

Transcription of nitrification genes by the methane-oxidizing bacterium, Methylococcus capsulatus strain Bath

Methylococcus capsulatus strain Bath, a methane-oxidizing bacterium, and ammonia-oxidizing bacteria (AOB) carry out the first step of nitrification, the oxidation of ammonia to nitrite, through the intermediate hydroxylamine. AOB use hydroxylamine oxidoreductase (HAO) to produce nitrite. M. capsulatus Bath was thought to oxidize hydroxylamine with cytochrome P460 (cytL), until the recent discovery of an hao gene in its genome. We used quantitative PCR analyses of cDNA from M. capsulatus Bath incubated with CH(4) or CH(4) plus 5 mM (NH(4))(2)SO(4) to determine whether cytL and hao transcript levels change in response to ammonia. While mRNA levels for cytL were not affected by ammonia, hao mRNA levels increased by 14.5- and 31-fold in duplicate samples when a promoter proximal region of the transcript was analyzed, and by sixfold when a region at the distal end of the transcript was analyzed. A conserved open reading frame, orf2, located 3' of hao in all known AOB genomes and in M. capsulatus Bath, was cotranscribed with hao and showed increased mRNA levels in the presence of ammonia. These data led to designating this gene pair as haoAB, with the role of haoB still undefined. We also determined mRNA levels for additional genes that encode proteins involved in N-oxide detoxification: cytochrome c'-beta (CytS) and nitric oxide (NO) reductase (NorCB). Whereas cytS mRNA levels increased in duplicate samples by 28.5- and 40-fold in response to ammonia, the cotranscribed norC-norB mRNA did not increase. Our results strongly suggest that M. capsulatus Bath possesses a functional, ammonia-responsive HAO involved in nitrification

Response of a Stoichiometrically Imbalanced Ecosystem to Manipulation of Nutrient Supplies and Ratios

Cuatro Ciénegas Basin (CCB) is a desert ecosystem that hosts a large diversity of water bodies. Many surface waters in this basin have imbalanced nitrogen (N) to phosphorus (P) stoichiometry (total N:P \u3e 100 by atoms), where P is likely to be a limiting nutrient. To investigate the effects of nutrient stoichiometry on planktonic and sediment ecosystem components and processes, we conducted a replicated in situ mesocosm experiment in Lagunita, a shallow pond located in the southwest region of the basin. Inorganic N and P were periodically added to mesocosms under three different N:P regimes (P only, N:P = 16 and N:P = 75) while the control mesocosms were left unamended. After three weeks of fertilization, more than two thirds of the applied P was immobilized into seston or sediment. The rapid uptake of P significantly decreased biomass C:P and N:P ratios, supporting the hypothesis that Lagunita is P-limited. Meanwhile, simultaneous N and P enrichment significantly enhanced planktonic growth, increasing total planktonic biomass by more than 2- fold compared to the unenriched control.With up to 76% of added N sequestered into the seston, it is suspected that the Lagunita microbial community also experienced strong Nlimitation. However, when N and P were applied at N:P = 75, the microbes remained in a P-limitation state as in the untreated control. Two weeks after the last fertilizer application, seston C:P and N:P ratios returned to initial levels but chlorophyll a and seston C concentrations remained elevated. Additionally, no P release from the sediment was observed in the fertilized mesocosms. Overall, this study provides evidence that Lagunita is highly sensitive to nutrient perturbation because the biota is primarily P-limited and experiences a secondary N-limitation despite its high TN:TP ratio. This study serves as a strong basis to justify the need for protection of CCB ecosystems and other low-nutrient microbedominated systems from anthropogenic inputs of both N and P

Fungal and bacterial communities of ‘Pinot noir’ must: effects of vintage, growing region, climate, and basic must chemistry

BackgroundThe geographic and temporal distributions of bacterial and fungal populations are poorly understood within the same wine grape cultivar. In this work, we describe the microbial composition from 'Pinot noir' must with respect to vintage, growing region, climate, and must chemistry across the states of California and Oregon, USA.Materials and methodsWe sampled 'Pinot noir' clone 667 clusters from 15 vineyards existing in a latitudinal gradient spanning nearly 1,200 km in California and Oregon for two vintages (2016 and 2017). Regions included five American Viticultural Areas (AVA). In order from southern California to Oregon, these AVAs were Santa Barbara, Monterey, Sonoma, Mendocino, and Willamette Valley. Uninoculated grape musts were subjected to 16S rRNA gene and ITS-1 amplicon sequencing to assess composition of microbial communities. We also measured grape maturity metrics. Finally, to describe regions by precipitation and growing degree days, we queried the Parameter-elevation Regressions on Independent Slopes Model (PRISM) spatial climate dataset.ResultsMost of the dominant bacterial taxa in must samples were in the family Enterobacteriaceae, notably the lactic acid bacteria or the acetic acid bacteria groups, but some, like the betaproteobacterial genus Massilia, belonged to groups not commonly found in grape musts. Fungal communities were dominated by Hanseniaspora uvarum (Saccharomycetaceae). We detected relationships between covariates (e.g., vintage, precipitation during the growing season, pH, titratable acidity, and total soluble solids) and bacterial genera Gluconobacter and Tatumella in the family Enterobacteraceae, Sphingomonas (Sphingomonodaceae), Lactobacillus (Lactobacillaceae), and Massilia (Oxalobacteraceae), as well as fungal genera in Hanseniaspora, Kazachstania, Lachancea, Torulaspora in the family Saccharomycetaceae, as well as Alternaria (Pleosporaceae), Erysiphe (Erysiphaceae), and Udeniomyces (Cystofilobasidiaceae). Fungal community distances were significantly correlated with geographic distances, but this was not observed for bacterial communities. Climate varied across regions and vintages, with growing season precipitation ranging from 11 mm to 285 mm and growing degree days ranging from 1,245 to 1,846.DiscussionWe determined that (1) bacterial beta diversity is structured by growing season precipitation, (2) fungal beta diversity reflects growing season precipitation and growing degree days, and (3) microbial differential abundances of specific genera vary with vintage, growing season precipitation, and fruit maturity metrics. Further, the correlation between fungal community dissimilarities and geographic distance suggests dispersal limitation and the vineyard as a source for abundant fungal taxa. Contrasting this observation, the lack of correlation between bacterial community dissimilarity and geographic distance suggests that environmental filtering is shaping these communities

N:P ratio of residual dissolved nutrients in the water column on days 21 and 42.

<p>Each bar represents average of 5 measurements ± 1 standard deviation. Different letters indicate significant differences between treatments for a given date while ‘*’ represents a significant change from day 21.</p

Physico-chemical characteristics of Lagunita prior to mesocosm installation in May 2011 (day 0), after 3-weeks of fertilizer application (day 21) and 3-weeks after fertilizer application was ceased (day 42).

<p>Values indicate the average of five measurements along the east-west transect ± 1 standard deviation. All values are in <i>μ</i>mol L^-1 unless otherwise stated. DOC: Dissolved organic carbon, SRP: Soluble reactive phosphorus, TDN: Total dissolved nitrogen, TDP: Total dissolved phosphorus. N.D.; Not determined.</p><p>^a Range from five location.</p><p>^b Range obtained from 24 hours continuous temperature loggers.</p><p>^c No replicate readings were taken.</p><p>Physico-chemical characteristics of Lagunita prior to mesocosm installation in May 2011 (day 0), after 3-weeks of fertilizer application (day 21) and 3-weeks after fertilizer application was ceased (day 42).</p

Effects of fertilizer application on sediment microbe biomass (separated cells) a) C:N, b) C:P, and c) N:P molar ratios for samples collected on day 21.

<p>Each bar represents the average of two measurements (three for NP16 treatment) ± 1 standard deviation.</p