Gene expression analysis of Alcaligenes faecalis during induction of heterotrophic nitrification

Metabolome-driven microbiome assembly determining the health of ginger crop (Zingiber officinale L. Roscoe) against rhizome rot

BACKGROUND

Plant-associated microorganisms can be found in various plant niches and collectively comprise the plant microbiome. The plant microbiome assemblages have been extensively studied, primarily in model species. However, a deep understanding of the microbiome assembly associated with plant health is still needed. Ginger rhizome rot has been variously attributed to multiple individual causal agents. Due to its global relevance, we used ginger and rhizome rot as a model to elucidate the metabolome-driven microbiome assembly associated with plant health.

RESULTS

Our study thoroughly examined the biodiversity of soilborne and endophytic microbiota in healthy and diseased ginger plants, highlighting the impact of bacterial and fungal microbes on plant health and the specific metabolites contributing to a healthy microbial community. Metabarcoding allowed for an in-depth analysis of the associated microbial community. Dominant genera represented each microbial taxon at the niche level. According to linear discriminant analysis effect size, bacterial species belonging to Sphingomonas, Quadrisphaera, Methylobacterium-Methylorubrum, Bacillus, as well as the fungal genera Pseudaleuria, Lophotrichus, Pseudogymnoascus, Gymnoascus, Mortierella, and Eleutherascus were associated with plant health. Bacterial dysbiosis related to rhizome rot was due to the relative enrichment of Pectobacterium, Alcaligenes, Klebsiella, and Enterobacter. Similarly, an imbalance in the fungal community was caused by the enrichment of Gibellulopsis, Pyxidiophorales, and Plectosphaerella. Untargeted metabolomics analysis revealed several metabolites that drive microbiome assembly closely related to plant health in diverse microbial niches. At the same time, 6-({[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)oxane-2,3,4,5-tetrol was present at the level of the entire healthy ginger plant. Lipids and lipid-like molecules were the most significant proportion of highly abundant metabolites associated with ginger plant health versus rhizome rot disease.

CONCLUSIONS

Our research significantly improves our understanding of metabolome-driven microbiome structure to address crop protection impacts. The microbiome assembly rather than a particular microbe's occurrence drove ginger plant health. Most microbial species and metabolites have yet to be previously identified in ginger plants. The indigenous microbial communities and metabolites described can support future strategies to induce plant disease resistance. They provide a foundation for further exploring pathogens, biocontrol agents, and plant growth promoters associated with economically important crops. Video Abstract.

Physiological adaptation and population dynamics of a nitrifying sludge exposed to ampicillin

Antibiotics in wastewater treatment plants can alter the physiological activity and the structure of microbial communities through toxic and inhibitory effects. Physiological adaptation, kinetic, and population dynamics behavior of a nitrifying sludge was evaluated in a sequential batch reactor (SBR) fed with 14.4 mg/L of ampicillin (AMP). The addition of AMP did not affect ammonium consumption (100 mg NH4+-N/L) but provoked nitrite accumulation (0.90 mg NO2--N formed/mg NH4+-N consumed) and an inhibition of up to 67% on the nitrite oxidizing process. After 30 cycles under AMP feeding, the sludge recovered its nitrite oxidizing activity with a high nitrate yield (YNO3-) of 0.87 ± 0.10 mg NO3--N formed/mg NH4+-N consumed, carrying out again a stable and complete nitrifying process. Increases in specific rate of nitrate production (qNO3-) showed the physiological adaptation of the nitrite oxidizing bacteria to AMP inhibition. Ampicillin was totally removed since the first cycle of addition. Exposure to AMP had effects on the abundance of bacterial populations, promoting adaptation of the nitrifying sludge to the presence of the antibiotic and its consumption. Nitrosomonas and Nitrosospira always remained within the dominant genera, keeping the ammonium oxidizing process stable while an increase in Nitrospira abundance was observed, recovering the stability of the nitrite oxidizing process. Burkholderia, Pseudomonas, and Thauera might be some of the heterotrophic bacteria involved in AMP consumption.

Hydroxylamine production by Alcaligenes faecalis challenges the paradigm of heterotrophic nitrification

Heterotrophic nitrifiers continue to be a hiatus in our understanding of the nitrogen cycle. Despite their discovery over 50 years ago, the physiology and environmental role of this enigmatic group remain elusive. The current theory is that heterotrophic nitrifiers are capable of converting ammonia to hydroxylamine, nitrite, nitric oxide, nitrous oxide, and dinitrogen gas via the subsequent actions of nitrification and denitrification. In addition, it was recently suggested that dinitrogen gas may be formed directly from ammonium. Here, we combine complementary high-resolution gas profiles, 15N isotope labeling studies, and transcriptomics data to show that hydroxylamine is the major product of nitrification in Alcaligenes faecalis. We demonstrated that denitrification and direct ammonium oxidation to dinitrogen gas did not occur under the conditions tested. Our results indicate that A. faecalis is capable of hydroxylamine production from an organic intermediate. These results fundamentally change our understanding of heterotrophic nitrification and have important implications for its biotechnological application.

Phylogenetic diversity, distribution, and gene structure of the pyruvic oxime dioxygenase involved in heterotrophic nitrification

Some heterotrophic microorganisms carry out nitrification to produce nitrite and nitrate from pyruvic oxime. Pyruvic oxime dioxygenase (POD) is an enzyme that catalyzes the degradation of pyruvic oxime to pyruvate and nitrite from the heterotrophic nitrifying bacterium Alcaligenes faecalis. Sequence similarity searches revealed the presence of genes encoding proteins homologous to A. faecalis POD in bacteria of the phyla Proteobacteria and Actinobacteria and in fungi of the phylum Ascomycota, and their gene products were confirmed to have POD activity in recombinant experiments. Phylogenetic analysis further classified these POD homologs into three groups. Group 1 POD is mainly found in heterotrophic nitrifying Betaproteobacteria and fungi, and is assumed to be involved in heterotrophic nitrification. It is not clear whether group 2 POD, found mainly in species of the Gammaproteobacteria and Actinobacteria, and group 3 POD, found simultaneously with group 1 POD, are involved in heterotrophic nitrification. The genes of bacterial group 1 POD comprised a single transcription unit with the genes related to the metabolism of aromatic compounds, and many of the genes group 2 POD consisted of a single transcription unit with the gene encoding the protein homologous to 4-hydroxy-tetrahydrodipicolinate synthase (DapA). LysR- or Cro/CI-type regulatory genes were present adjacent to or in the vicinity of these POD gene clusters. POD may be involved not only in nitrification, but also in certain metabolic processes whose functions are currently unknown, in coordination with members of gene clusters.

Alcaligenes ammonioxydans HO-1 antagonizes Bacillus velezensis via hydroxylamine-triggered population response

Antagonism is a common behavior seen between microbes in nature. Alcaligenes ammonioxydans HO-1 converts ammonia to nitrogen under aerobic conditions, which leads to the accumulation of extracellular hydroxylamine (HA), providing pronounced growth advantages against many bacterial genera, including Bacillus velezensis V4. In contrast, a mutant variant of A. ammonioxydans, strain 2-29, that cannot produce HA fails to antagonize other bacteria. In this article, we demonstrate that cell-free supernatants derived from the antagonistic HO-1 strain were sufficient to reproduce the antagonistic behavior and the efficiency of this inhibition correlated strongly with the HA content of the supernatant. Furthermore, reintroducing the capacity to produce HA to the 2-29 strain or supplementing bacterial co-cultures with HA restored antagonistic behavior. The HA-mediated antagonism was dose-dependent and affected by the temperature, but not by pH. HA caused a decline in biomass, cell aggregation, and hydrolysis of the cell wall in exponentially growing B. velezensis bulk cultures. Analysis of differential gene expression identified a series of genes modulating multicellular behavior in B. velezensis. Genes involved in motility, chemotaxis, sporulation, polypeptide synthesis, and non-ribosomal peptide synthesis were all significantly downregulated in the presence of HA, whereas autolysis-related genes showed upregulation. Taken together, these findings indicate that HA affects the population response of coexisting strains and also suggest that A. ammonioxydans HO-1 antagonize other bacteria by producing extracellular HA that, in turn, acts as a signaling molecule.