-
The ISME Journal Apr 2020Zetaproteobacteria are obligate chemolithoautotrophs that oxidize Fe(II) as an electron and energy source, and play significant roles in nutrient cycling and primary...
Zetaproteobacteria are obligate chemolithoautotrophs that oxidize Fe(II) as an electron and energy source, and play significant roles in nutrient cycling and primary production in the marine biosphere. Zetaproteobacteria thrive under microoxic conditions near oxic-anoxic interfaces, where they catalyze Fe(II) oxidation faster than the abiotic reaction with oxygen. Neutrophilic Fe(II) oxidizing bacteria produce copious amounts of insoluble iron oxyhydroxides as a by-product of their metabolism. Oxygen consumption by aerobic respiration and formation of iron oxyhydroxides at oxic-anoxic interfaces can result in periods of oxygen limitation for bacterial cells. Under laboratory conditions, all Zetaproteobacteria isolates have been shown to strictly require oxygen as an electron acceptor for growth, and anaerobic metabolism has not been observed. However, genomic analyses indicate a range of potential anaerobic pathways present in Zetaproteobacteria. Heterologous expression of proteins from Mariprofundus ferrooxydans PV-1, including pyruvate formate lyase and acetate kinase, further support a capacity for anaerobic metabolism. Here we define auxiliary anaerobic metabolism as a mechanism to provide maintenance energy to cells and suggest that it provides a survival advantage to Zetaproteobacteria in environments with fluctuating oxygen availability.
Topics: Anaerobiosis; Ferric Compounds; Oxidation-Reduction; Oxygen; Proteobacteria; Seawater
PubMed: 31969684
DOI: 10.1038/s41396-020-0586-6 -
Microbiology Spectrum Oct 2021The geological role of microorganisms has been widely studied in the karst cave ecosystem. However, microbial interactions and ecological functions in such a dark,...
The geological role of microorganisms has been widely studied in the karst cave ecosystem. However, microbial interactions and ecological functions in such a dark, humid, and oligotrophic habitat have received far less attention, which is crucial to understanding cave biogeochemistry. Herein, microorganisms from weathered rock and sediment along the Heshang Cave depth were analyzed by random matrix theory-based network and Tax4Fun functional prediction. The results showed that although the cave microbial communities have spatial heterogeneity, differential habitats drove the community structure and diversity. were predominant in weathered rock, whereas dominated the sediment. The sediment communities presented significantly higher alpha diversities due to the relatively abundant nutrition from the outside by the intermittent stream. Consistently, microbial interactions in sediment were more complex, as visualized by more nodes and links. The abundant taxa presented more positive correlations with other community members in both of the two networks, indicating that they relied on promotion effects to adapt to the extreme environment. The keystones in weathered rock were mainly involved in the biodegradation of organic compounds, whereas the keystone in sediment contributed to carbon/nitrogen fixation. Collectively, these findings suggest that microbial interactions may lead to distinct taxonomic and functional communities in weathered rock and sediment in the subsurface Heshang Cave. In general, the constant physicochemical conditions and limited nutrient sources over long periods in the subsurface support a stable ecosystem in karst cave. Previous studies on cave microbial ecology were mostly focused on community composition, diversity, and the relationship with local environmental factors. There are still many unknowns about the microbial interactions and functions in such a dark environment with little human interference. Two representative habitats, including weathered rock and sediment in Heshang Cave, were selected to give an integrated insight into microbial interactions and potential functions. The cooccurrence network, especially the subnetwork, was used to characterize the cave microbial interactions in detail. We demonstrated that abundant taxa primarily relied on promotion effects rather than inhibition effects to survive in Heshang Cave. Keystone species may play important metabolic roles in sustaining ecological functions. Our study provides improved understanding of microbial interaction patterns and community ecological functions in the karst cave ecosystem.
Topics: Actinobacteria; Bacterial Physiological Phenomena; Carbon Cycle; Caves; Ecosystem; Geologic Sediments; Microbial Interactions; Nitrogen Fixation; Proteobacteria; Soil Microbiology
PubMed: 34494852
DOI: 10.1128/Spectrum.01152-21 -
PLoS Biology Mar 2019Bacteria switch only intermittently to motile planktonic lifestyles under favorable conditions. Under chronic nutrient deprivation, however, bacteria orchestrate a...
Bacteria switch only intermittently to motile planktonic lifestyles under favorable conditions. Under chronic nutrient deprivation, however, bacteria orchestrate a switch to stationary phase, conserving energy by altering metabolism and stopping motility. About two-thirds of bacteria use flagella to swim, but how bacteria deactivate this large molecular machine remains unclear. Here, we describe the previously unreported ejection of polar motors by γ-proteobacteria. We show that these bacteria eject their flagella at the base of the flagellar hook when nutrients are depleted, leaving a relic of a former flagellar motor in the outer membrane. Subtomogram averages of the full motor and relic reveal that this is an active process, as a plug protein appears in the relic, likely to prevent leakage across their outer membrane; furthermore, we show that ejection is triggered only under nutritional depletion and is independent of the filament as a possible mechanosensor. We show that filament ejection is a widespread phenomenon demonstrated by the appearance of relic structures in diverse γ-proteobacteria including Plesiomonas shigelloides, Vibrio cholerae, Vibrio fischeri, Shewanella putrefaciens, and Pseudomonas aeruginosa. While the molecular details remain to be determined, our results demonstrate a novel mechanism for bacteria to halt costly motility when nutrients become scarce.
Topics: Flagella; Gammaproteobacteria; Plesiomonas; Pseudomonas aeruginosa; Shewanella putrefaciens; Vibrio cholerae
PubMed: 30889173
DOI: 10.1371/journal.pbio.3000165 -
Journal of Applied Microbiology Jan 2013To explore rhizospheric microbial communities from Arctic native plant species evaluating their bacterial hydrocarbon-degrading capacities.
AIMS
To explore rhizospheric microbial communities from Arctic native plant species evaluating their bacterial hydrocarbon-degrading capacities.
METHODS AND RESULTS
Eriophorum scheuchzeri, Potentilla cf. rubricaulis, Oxyria digyna, Salix arctica and Puccinellia angustata plant species were collected at Eureka (Canadian high Arctic) along with their rhizospheric soil samples. Their bacterial community fingerprints (16S rRNA gene, DGGE) were distinctive encompassing members from the phyla: Bacteroidetes, Firmicutes, Actinobacteria and Proteobacteria. Isolated diesel-degrading bacteria belonged to the phyla Actinobacteria and Proteobacteria. Strains of Mycobacterium, Nocardia, Rhodococcus, Intrasporangiaceae, Leifsoni and Arthrobacter possessed alkB and Pseudomonas possessed both ndoB and xylE gene sequences. Two Rhodococcus strains mineralized [1-(14) C] hexadecane at 5 and -5°C. From the rhizosphere of P. angustata, larger numbers of hydrocarbon-degrading bacteria were isolated than from other plant rhizosphere samples and all three genes alkB (from Actinobacteria), ndoB and xylE (from Pseudomonas) were detected by PCR.
CONCLUSIONS
(i) Arctic plants have unique rhizospheric bacterial communities. (ii) P. angustata has potential for phytoremediation research at high Arctic soils. (iii) Isolated bacteria mineralized hydrocarbons at ambient low temperatures.
SIGNIFICANCE AND IMPACT OF THE STUDY
To the best of our knowledge, this is the first rhizospheric exploration examining the phytoremediation potential of five Arctic plants and evaluating their microbial hydrocarbon-degrading capacities.
Topics: Actinobacteria; Alkanes; Arctic Regions; Biodegradation, Environmental; Canada; Colony Count, Microbial; Genes, Bacterial; Hydrocarbons; Magnoliopsida; Phylogeny; Proteobacteria; RNA, Ribosomal, 16S; Rhizosphere; Soil; Soil Microbiology; Soil Pollutants
PubMed: 22984892
DOI: 10.1111/jam.12020 -
Research in Microbiology 2018The proteobacterial antimicrobial compound efflux (PACE) family of transport proteins was only recently described. PACE family transport proteins can confer resistance... (Review)
Review
The proteobacterial antimicrobial compound efflux (PACE) family of transport proteins was only recently described. PACE family transport proteins can confer resistance to a range of biocides used as disinfectants and antiseptics, and are encoded by many important Gram-negative human pathogens. However, we are only just beginning to appreciate the range of functions and the mechanism(s) of transport operating in these proteins. Genes encoding PACE family proteins are typically conserved in the core genomes of bacterial species rather than on recently acquired mobile genetic elements, suggesting that they confer important core functions in addition to biocide resistance. Three-dimensional structural information is not yet available for PACE family proteins. However, PACE proteins have several very highly conserved amino acid sequence motifs that are likely to be important for substrate transport. PACE proteins also display strong amino acid sequence conservation between their N and C-terminal halves, suggesting that they evolved by duplication of an ancestral protein comprised of two transmembrane helices. In light of their drug resistance functions in Gram-negative pathogens, PACE proteins should be the subject of detailed future investigation.
Topics: Anti-Bacterial Agents; Bacterial Proteins; Biological Transport; Disinfectants; Gram-Negative Bacteria; Membrane Transport Proteins; Multigene Family; Proteobacteria
PubMed: 29409983
DOI: 10.1016/j.resmic.2018.01.001 -
Applied and Environmental Microbiology Mar 2000PCR primers were patterned after chitinase genes in four gamma-proteobacteria in the families Alteromonadaceae and Enterobacteriaceae (group I chitinases) and used to...
PCR primers were patterned after chitinase genes in four gamma-proteobacteria in the families Alteromonadaceae and Enterobacteriaceae (group I chitinases) and used to explore the occurrence and diversity of these chitinase genes in cultured and uncultured marine bacteria. The PCR results from 104 bacterial strains indicated that this type of chitinase gene occurs in two major groups of marine bacteria, alpha- and gamma-proteobacteria, but not the Cytophaga-Flavobacter group. Group I chitinase genes also occur in some viruses infecting arthropods. Phylogenetic analysis indicated that similar group I chitinase genes occur in taxonomically related bacteria. However, the overall phylogeny of chitinase genes did not correspond to the phylogeny of 16S rRNA genes, possibly due to lateral transfer of chitinase genes between groups of bacteria, but other mechanisms, such as gene duplication, cannot be ruled out. Clone libraries of chitinase gene fragments amplified from coastal Pacific Ocean and estuarine Delaware Bay bacterioplankton revealed similarities and differences between cultured and uncultured bacteria. We had hypothesized that cultured and uncultured chitin-degrading bacteria would be very different, but in fact, clones having nucleotide sequences identical to those of chitinase genes of cultured alpha-proteobacteria dominated both libraries. The other clones were similar but not identical to genes in cultured gamma-proteobacteria, including vibrios and alteromonads. Our results suggest that a closer examination of chitin degradation by alpha-proteobacteria will lead to a better understanding of chitin degradation in the ocean.
Topics: Alphaproteobacteria; Atlantic Ocean; Chitin; Chitinases; Cloning, Molecular; DNA Primers; Delaware; Gammaproteobacteria; Genes, Bacterial; Molecular Sequence Data; Phylogeny; Seawater; Sequence Analysis, DNA
PubMed: 10698791
DOI: 10.1128/AEM.66.3.1195-1201.2000 -
PloS One 2018Studies about the composition and diversity of microbial community in the Rare Earth Elements-rich muds are limited. In this research, we conducted a characterization...
Studies about the composition and diversity of microbial community in the Rare Earth Elements-rich muds are limited. In this research, we conducted a characterization for the composition and diversity of bacterial and archaeal communities from rare earth elements-rich gravity core sediment at approximately 4800 meters deep in the Indian Ocean by Illumina high-throughput sequencing targeting 16S rRNA genes. The results showed that the most abundant bacteria were Proteobacteria, followed by Firmicutes and Actinobacteria. Amongst Proteobacteria, Gammaproteobacteria are present in all sections of this sediment core accounted for a particularly large proportion of bacterial sequences. Candidatus Nitrosopumilus, with a higher relative abundance in our samples, belongs to Thaumarchaeota. This is the first report on the composition and diversity of rare earth elements-rich muds microbial communities in the Indian Ocean deep sea.
Topics: Actinobacteria; Archaea; Bacteria; Firmicutes; Gammaproteobacteria; Microbiota; Proteobacteria; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA
PubMed: 30557300
DOI: 10.1371/journal.pone.0208230 -
MicrobiologyOpen Apr 2013Insect fungiculture is practiced by ants, termites, beetles, and gall midges and it has been suggested to be widespread among plant-ants. Some of the insects engaged in...
Insect fungiculture is practiced by ants, termites, beetles, and gall midges and it has been suggested to be widespread among plant-ants. Some of the insects engaged in fungiculture, including attine ants and bark beetles, are known to use symbiotic antibiotic-producing actinobacteria to protect themselves and their fungal cultivars against infection. In this study, we analyze the bacterial communities on the cuticles of the plant-ant genera Allomerus and Tetraponera using deep sequencing of 16S rRNA. Allomerus ants cultivate fungus as a building material to strengthen traps for prey, while Tetraponera ants cultivate fungus as a food source. We report that Allomerus and Tetraponera microbiomes contain >75% Proteobacteria and remarkably the bacterial phyla that dominate their cuticular microbiomes are very similar despite their geographic separation (South America and Africa, respectively). Notably, antibiotic-producing actinomycete bacteria represent a tiny fraction of the cuticular microbiomes of both Allomerus and Tetraponera spp. and instead they are dominated by γ-proteobacteria Erwinia and Serratia spp. Both these phyla are known to contain antibiotic-producing species which might therefore play a protective role in these ant-plant systems.
Topics: Actinobacteria; Africa; Animals; Ants; Bacteria; Erwinia; Fungi; Metagenome; Plants; Proteobacteria; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Serratia; Soil Microbiology; South America; Symbiosis
PubMed: 23417898
DOI: 10.1002/mbo3.73 -
MBio Mar 2019Many species of proteobacteria communicate with kin and coordinate group behaviors through a form of cell-cell signaling called acyl-homoserine lactone (AHL) quorum...
Many species of proteobacteria communicate with kin and coordinate group behaviors through a form of cell-cell signaling called acyl-homoserine lactone (AHL) quorum sensing (QS). Most AHL receptors are thought to be specific for their cognate signal, ensuring that bacteria cooperate and share resources only with closely related kin cells. Although specificity is considered fundamental to QS, there are reports of "promiscuous" receptors that respond broadly to nonself signals. These promiscuous responses expand the function of QS systems to include interspecies interactions and have been implicated in both interspecies competition and cooperation. Because bacteria are frequently members of polymicrobial communities, AHL cross talk between species could have profound impacts. To better understand the prevalence of QS promiscuity, we measured the activity of seven QS receptors in their native host organisms. To facilitate comparison of our results to previous studies, we also measured receptor activity using heterologous expression in We found that the standard methods consistently overestimate receptor promiscuity and sensitivity and that overexpression of the receptors is sufficient to account for the discrepancy between native and reporters. Additionally, receptor overexpression resulted in AHL-independent activity in Using our activation data, we developed a quantitative score of receptor selectivity. We find that the receptors display a wide range of selectivity and that most receptors respond sensitively and strongly to at least one nonself signal, suggesting a broad potential for cross talk between QS systems. Specific recognition of cognate signals is considered fundamental to cell signaling circuits as it creates fidelity in the communication system. In bacterial quorum sensing (QS), receptor specificity ensures that bacteria cooperate only with kin. There are examples, however, of QS receptors that respond promiscuously to multiple signals. "Eavesdropping" by these promiscuous receptors can be beneficial in both interspecies competition and cooperation. Despite their potential significance, we know little about the prevalence of promiscuous QS receptors. Further, many studies rely on methods requiring receptor overexpression, which is known to increase apparent promiscuity. By systematically studying QS receptors in their natural parent strains, we find that the receptors display a wide range of selectivity and that there is potential for significant cross talk between QS systems. Our results provide a basis for hypotheses about the evolution and function of promiscuous signal receptors and for predictions about interspecies interactions in complex microbial communities.
Topics: Acyl-Butyrolactones; Gene Expression Regulation, Bacterial; Microbial Interactions; Proteobacteria; Quorum Sensing
PubMed: 30837333
DOI: 10.1128/mBio.00146-19 -
Microbial Ecology Jan 2015A combined approach, using molecular and microscopic techniques, was used to identify the microbiota associated with the Archimedes Palimpsest, an unusual parchment...
A combined approach, using molecular and microscopic techniques, was used to identify the microbiota associated with the Archimedes Palimpsest, an unusual parchment manuscript. SEM analyses revealed the microbial damage to the collagen fibers and the presence of characteristic cell chains typical of filamentous bacteria and fungal spores. Molecular analysis confirmed a homogeneous bacterial community colonizing the manuscript. The phyla Proteobacteria and Actinobacteria were associated with this ancient parchment; the sequences were most related to uncultured clones detected in the human skin microbiome and in ephitelium, and to cultivated species of the genera Acinetobacter and Nocardiopsis. Nevertheless, a great variation was observed among the different sampled areas indicating fungal diversity. Blumeria spp. dominated in the healthy areas of the parchment while degraded areas showed disparate fungal communities, with dominant members of the genera Mucor and Cladosporium. In addition, the quantification of the β-actin gene by real-time PCR analyses (qPCR) revealed a higher fungal abundance on degraded areas than on the healthy ones.
Topics: Actinobacteria; Biodiversity; Environmental Microbiology; Fungi; Proteobacteria; RNA, Ribosomal, 16S; Real-Time Polymerase Chain Reaction
PubMed: 25135817
DOI: 10.1007/s00248-014-0481-7