Acyl-Homoserine Lactone Production in Nitrifying Bacteria of the Genera Nitrosospira, Nitrobacter, and Nitrospira Identified via a Survey of Putative Quorum-Sensing Genes

Abstract

The genomes of many bacteria that participate in nitrogen cycling through the process of nitrification contain putative genes associated with acyl-homoserine lactone (AHL) quorum sensing (QS). AHL QS or bacterial cell-cell signaling is a method of bacterial communication and gene regulation and may be involved in nitrogen oxide fluxes or other important phenotypes in nitrifying bacteria. Here, we carried out a broad survey of AHL production in nitrifying bacteria in three steps. First, we analyzed the evolutionary history of AHL synthase and AHL receptor homologs in sequenced genomes and metagenomes of nitrifying bacteria to identify AHL synthase homologs in ammonia-oxidizing bacteria (AOB) of the genus and nitrite-oxidizing bacteria (NOB) of the genera, , and Next, we screened cultures of both AOB and NOB with uncharacterized AHL synthase genes and AHL synthase-negative nitrifiers by a bioassay. Our results suggest that an AHL synthase gene is required for, but does not guarantee, cell density-dependent AHL production under the conditions tested. Finally, we utilized mass spectrometry to identify the AHLs produced by the AOB and and the NOB and as -decanoyl-l-homoserine lactone (C-HSL), -3-hydroxy-tetradecanoyl-l-homoserine lactone (3-OH-C-HSL), a monounsaturated AHL (C-HSL), and -octanoyl-l-homoserine lactone (C-HSL), respectively. Our survey expands the list of AHL-producing nitrifiers to include a representative of lineage II and suggests that AHL production is widespread in nitrifying bacteria. Nitrification, the aerobic oxidation of ammonia to nitrate via nitrite by nitrifying microorganisms, plays an important role in environmental nitrogen cycling from agricultural fertilization to wastewater treatment. The genomes of many nitrifying bacteria contain genes associated with bacterial cell-cell signaling or quorum sensing (QS). QS is a method of bacterial communication and gene regulation that is well studied in bacterial pathogens, but less is known about QS in environmental systems. Our previous work suggested that QS might be involved in the regulation of nitrogen oxide gas production during nitrite metabolism. This study characterized putative QS signals produced by different genera and species of nitrifiers. Our work lays the foundation for future experiments investigating communication between nitrifying bacteria, the purpose of QS in these microorganisms, and the manipulation of QS during nitrification.

Genomic Analysis of Two Phylogenetically Distinct Nitrospira Species Reveals Their Genomic Plasticity and Functional Diversity

“…Comparing genomic features among Nitrospira strains, we first focused on the genes involved in nitrogen metabolism, such as nitrite reduction and urea degradation. Next, from the strain NJ1 genome, we discovered the key genes of acyl-homoserine lactone (AHL)-type quorum-sensing (QS) systems, which was reported in the previous study ( Nasuno et al, 2012 ; Mellbye et al, 2017 ), and we identified the chemical structures of the AHLs as autoinducers of strain NJ1. Moreover, the genome sequence of strain NJ1 lacks genes encoding bacterial flagella and CRISPR-Cas system, which were reported in genomic analyses of other Nitrospira ( Figure 2 ).…”

“…Recently, it was reported that the genome sequence of N. moscoviensis, N. inopinata , and Ca . Nitrospira nitrificans contains a gene encoding AHL synthase homologs ( Mellbye et al, 2017 ). Phylogenetic analysis based on the amino acid sequence of autoinducer synthases revealed that the LuxI homologs of Nitrospira were each clustered into single clades ( Figure 5 ), and that NjpI, a LuxI homolog in strain NJ1, was most closely related to that of Ca.…”

Genomic profiling of four cultivated Candidatus Nitrotoga spp. predicts broad metabolic potential and environmental distribution

“…Other NOB have been documented to use quorum sensing at high cell densities and the Ca. Nitrotoga LuxI homolog grouped phylogenetically with other sequenced Betaproteobacteria [111,112]. Ca.…”

Microbial Origin of Excreted DNA in Particular Fractions of Extracellular Polymers (EPS) in Aerobic Granules

“…Moreover, nitrifying bacteria do not produce enough EPS and barely achieved self-immobilization, so they were probably attached to EPS produced by other microorganisms. Since QS is responsible for bacteria communication and gene regulation during nitrification, the conditions in TB-EPS seem to be more favorable for nitrifying bacteria (Mellbye et al 2017).…”