Heritability and Functional Importance of the Setaria viridis Bacterial Seed Microbiome

Seed-associated bacteria represent an important reservoir of microorganisms passed onto progeny plants and have been postulated to be important for early plant development and early plant vigor. According to a few reports, some bacterial taxa seem to be transferred from seed to seed and some seed-associated microorganisms may derive from insect visits during flowering; however, the origin of seed endophytes is poorly understood. To better understand the origin, ecology, and functional role of seed bacterial endophytes, we planted Setaria viridis seeds over several generations in a sterile growth substrate. Seed microbiota of each generation were analyzed by next generation sequencing of 16S rRNA genes and seeds were characterized regarding to their germination and plant growth. Growing plants in a sterile (or highly depleted) substrate resulted in seed microbiota, which were largely less diverse and which had altered community composition, particularly at later generations, indicating that soil is an important reservoir of seed microbiota. Some taxa were inherited to the next generations seeds; however, different subsets of taxa were inherited in different seeds/seed batches and across different generations. This suggests that other factors than the host control the establishment of most seed endophytes and only few, e.g., obligate endophytes, might be consistently inherited. Furthermore, we observed a drastic decline in seed vigor and later generations were particularly affected. Overall, our results demonstrated that the supply of endophytes from external sources such as the soil/rhizosphere environment is highly important for the build-up of a healthy seed microbiome warranting early plant establishment and vigor of next generation plants.

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Role of Broiler Carcasses and Processing Plant Air in Contamination of Modified-Atmosphere-Packaged Broiler Products with Psychrotrophic Lactic Acid Bacteria

Applied and Environmental Microbiology ◽

10.1128/aem.01644-06 ◽

2006 ◽

Vol 73 (4) ◽

pp. 1136-1145 ◽

Cited By ~ 55

Author(s):

Elina Vihavainen ◽

Hanna-Saara Lundstrï¿½m ◽

Tuija Susiluoto ◽

Joanna Koort ◽

Lars Paulin ◽

...

Keyword(s):

Lactic Acid ◽

Lactic Acid Bacteria ◽

16S Rrna Genes ◽

Rrna Genes ◽

23S Rrna ◽

Processing Plant ◽

Modified Atmosphere ◽

Production Plant ◽

Meat Spoilage

ABSTRACT Some psychrotrophic lactic acid bacteria (LAB) are specific meat spoilage organisms in modified-atmosphere-packaged (MAP), cold-stored meat products. To determine if incoming broilers or the production plant environment is a source of spoilage LAB, a total of 86, 122, and 447 LAB isolates from broiler carcasses, production plant air, and MAP broiler products, respectively, were characterized using a library of HindIII restriction fragment length polymorphism (RFLP) patterns of the 16 and 23S rRNA genes as operational taxonomic units in numerical analyses. Six hundred thirteen LAB isolates from the total of 655 clustered in 29 groups considered to be species specific. Sixty-four percent of product isolates clustered either with Carnobacterium divergens or with Carnobacterium maltaromaticum type strains. The third major product-associated cluster (17% of isolates) was formed by unknown LAB. Representative strains from these three clusters were analyzed for the phylogeny of their 16S rRNA genes. This analysis verified that the two largest RFLP clusters consisted of carnobacteria and showed that the unknown LAB group consisted of Lactococcus spp. No product-associated LAB were detected in broiler carcasses sampled at the beginning of slaughter, whereas carnobacteria and lactococci, along with some other specific meat spoilage LAB, were recovered from processing plant air at many sites. This study reveals that incoming broiler chickens are not major sources of psychrotrophic spoilage LAB, whereas the detection of these organisms from the air of the processing environment highlights the role of processing facilities as sources of LAB contamination.

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Coaggregation among Nonflocculating Bacteria Isolated from Activated Sludge

Applied and Environmental Microbiology ◽

10.1128/aem.69.10.6056-6063.2003 ◽

2003 ◽

Vol 69 (10) ◽

pp. 6056-6063 ◽

Cited By ~ 91

Author(s):

Anushree Malik ◽

Masashi Sakamoto ◽

Shohei Hanazaki ◽

Masamitsu Osawa ◽

Takanori Suzuki ◽

...

Keyword(s):

16S Rrna ◽

Activated Sludge ◽

Aggregate Size ◽

Spectrophotometric Assay ◽

Full Length ◽

16S Rrna Genes ◽

Rrna Genes ◽

Acinetobacter Junii ◽

Acinetobacter Johnsonii

ABSTRACT Thirty-two strains of nonflocculating bacteria isolated from sewage-activated sludge were tested by a spectrophotometric assay for their ability to coaggregate with one other in two-membered systems. Among these strains, eight showed significant (74 to 99%) coaggregation with Acinetobacter johnsonii S35 while only four strains coaggregated, to a lesser extent (43 to 65%), with Acinetobacter junii S33. The extent and pattern of coaggregation as well as the aggregate size showed good correlation with cellular characteristics of the coaggregating partners. These strains were identified by sequencing of full-length 16S rRNA genes. A. johnsonii S35 could coaggregate with strains of several genera, such as Oligotropha carboxidovorans, Microbacterium esteraromaticum, and Xanthomonas spp. The role of Acinetobacter isolates as bridging organisms in multigeneric coaggregates is indicated. This investigation revealed the role of much-neglected nonflocculating bacteria in floc formation in activated sludge.

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The Xylella fastidiosa-Resistant Olive Cultivar “Leccino” Has Stable Endophytic Microbiota during the Olive Quick Decline Syndrome (OQDS)

Pathogens ◽

10.3390/pathogens9010035 ◽

2019 ◽

Vol 9 (1) ◽

pp. 35 ◽

Cited By ~ 7

Author(s):

Marzia Vergine ◽

Joana B. Meyer ◽

Massimiliano Cardinale ◽

Erika Sabella ◽

Martin Hartmann ◽

...

Keyword(s):

Xylella Fastidiosa ◽

Resistance Mechanisms ◽

16S Rrna Genes ◽

Rrna Genes ◽

Olive Cultivar ◽

Olive Quick Decline Syndrome ◽

Olive Trees ◽

Potential Interactions ◽

Highly Virulent

Xylella fastidiosa is a highly virulent pathogen that causes Olive Quick Decline Syndrome (OQDS), which is currently devastating olive plantations in the Salento region (Apulia, Southern Italy). We explored the microbiome associated with X. fastidiosa-infected (Xf-infected) and -uninfected (Xf-uninfected) olive trees in Salento, to assess the level of dysbiosis and to get first insights into the potential role of microbial endophytes in protecting the host from the disease. The resistant cultivar “Leccino” was compared to the susceptible cultivar “Cellina di Nardò”, in order to identify microbial taxa and parameters potentially involved in resistance mechanisms. Metabarcoding of 16S rRNA genes and fungal ITS2 was used to characterize both total and endophytic microbiota in olive branches and leaves. “Cellina di Nardò” showed a drastic dysbiosis after X. fastidiosa infection, while “Leccino” (both infected and uninfected) maintained a similar microbiota. The genus Pseudomonas dominated all “Leccino” and Xf-uninfected “Cellina di Nardò” trees, whereas Ammoniphilus prevailed in Xf-infected “Cellina di Nardò”. Diversity of microbiota in Xf-uninfected “Leccino” was higher than in Xf-uninfected “Cellina di Nardò”. Several bacterial taxa specifically associated with “Leccino” showed potential interactions with X. fastidiosa. The maintenance of a healthy microbiota with higher diversity and the presence of cultivar-specific microbes might support the resistance of “Leccino” to X. fastidiosa. Such beneficial bacteria might be isolated in the future for biological treatment of the OQDS.

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Metagenomic Pyrosequencing and Microbial Identification

Clinical Chemistry ◽

10.1373/clinchem.2008.107565 ◽

2009 ◽

Vol 55 (5) ◽

pp. 856-866 ◽

Cited By ~ 330

Author(s):

Joseph F Petrosino ◽

Sarah Highlander ◽

Ruth Ann Luna ◽

Richard A Gibbs ◽

James Versalovic

Keyword(s):

Human Microbiome ◽

Human Microbiome Project ◽

Amplicon Sequencing ◽

16S Rrna Genes ◽

Rrna Genes ◽

Next Generation ◽

New Era ◽

Microbial Identification ◽

Core Technology ◽

Dna Pyrosequencing

Abstract Background: The Human Microbiome Project has ushered in a new era for human metagenomics and high-throughput next-generation sequencing strategies. Content: This review describes evolving strategies in metagenomics, with a special emphasis on the core technology of DNA pyrosequencing. The challenges of microbial identification in the context of microbial populations are discussed. The development of next-generation pyrosequencing strategies and the technical hurdles confronting these methodologies are addressed. Bioinformatics-related topics include taxonomic systems, sequence databases, sequence-alignment tools, and classifiers. DNA sequencing based on 16S rRNA genes or entire genomes is summarized with respect to potential pyrosequencing applications. Summary: Both the approach of 16S rDNA amplicon sequencing and the whole-genome sequencing approach may be useful for human metagenomics, and numerous bioinformatics tools are being deployed to tackle such vast amounts of microbiological sequence diversity. Metagenomics, or genetic studies of microbial communities, may ultimately contribute to a more comprehensive understanding of human health, disease susceptibilities, and the pathophysiology of infectious and immune-mediated diseases.

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Investigation of Sources, Diversity, and Variability of Bacterial Aerosols in Athens, Greece: A Pilot Study

Atmosphere ◽

10.3390/atmos13010045 ◽

2021 ◽

Vol 13 (1) ◽

pp. 45

Author(s):

Angelina Metaxatos ◽

Sydonia Manibusan ◽

Gediminas Mainelis

Keyword(s):

Field Application ◽

16S Rrna Genes ◽

Rrna Genes ◽

Airborne Bacteria ◽

Urban Air ◽

Operational Taxonomic Units ◽

Bacterial Aerosol ◽

Bacterial Aerosols ◽

Taxonomic Categories

We characterized the composition, diversity, and potential bacterial aerosol sources in Athens’ urban air by DNA barcoding (analysis of 16S rRNA genes) during three seasons in 2019. Air samples were collected using the recently developed Rutgers Electrostatic Passive Sampler (REPS). It is the first field application of REPS to study bacterial aerosol diversity. REPS samplers captured a sufficient amount of biological material to demonstrate the diversity of airborne bacteria and their variability over time. Overall, in the air of Athens, we detected 793 operational taxonomic units (OTUs), which were fully classified into the six distinct taxonomic categories (Phylum, Class, Order, etc.). These OTUs belonged to Phyla Actinobacteria, Firmicutes, Proteobacteria, Bacteroidetes, Cyanobacteria, and Fusobacteria. We found a complex community of bacterial aerosols with several opportunistic or potential pathogens in Athens’ urban air. Referring to the available literature, we discuss the likely sources of observed airborne bacteria, including soil, plants, animals, and humans. Our results on bacterial diversity are comparable to earlier studies, even though the sampling sites are different or geographically distant. However, the exact functional and ecological role of bioaerosols and, even more importantly, their impact on public health and the ecosystem requires further air monitoring and analysis.

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Metagenomic Analysis of Slovak Bryndza Cheese Using Next-Generation 16S rDNA Amplicon Sequencing

Nova Biotechnologica et Chimica ◽

10.1515/nbec-2016-0003 ◽

2016 ◽

Vol 15 (1) ◽

pp. 23-34 ◽

Cited By ~ 7

Author(s):

Matej Planý ◽

Tomáš Kuchta ◽

Katarína Šoltýs ◽

Tomáš Szemes ◽

Domenico Pangallo ◽

...

Keyword(s):

16S Rrna ◽

16S Rdna ◽

Lactococcus Lactis ◽

Microbial Population ◽

Starter Culture ◽

Amplicon Sequencing ◽

16S Rrna Genes ◽

Rrna Genes ◽

Next Generation ◽

16S Rdna Amplicon Sequencing

Abstract Knowledge about diversity and taxonomic structure of the microbial population present in traditional fermented foods plays a key role in starter culture selection, safety improvement and quality enhancement of the end product. Aim of this study was to investigate microbial consortia composition in Slovak bryndza cheese. For this purpose, we used culture-independent approach based on 16S rDNA amplicon sequencing using next generation sequencing platform. Results obtained by the analysis of three commercial (produced on industrial scale in winter season) and one traditional (artisanal, most valued, produced in May) Slovak bryndza cheese sample were compared. A diverse prokaryotic microflora composed mostly of the genera Lactococcus, Streptococcus, Lactobacillus, and Enterococcus was identified. Lactococcus lactis subsp. lactis and Lactococcus lactis subsp. cremoris were the dominant taxons in all tested samples. Second most abundant species, detected in all bryndza cheeses, were Lactococcus fujiensis and Lactococcus taiwanensis, independently by two different approaches, using different reference 16S rRNA genes databases (Greengenes and NCBI respectively). They have been detected in bryndza cheese samples in substantial amount for the first time. The narrowest microbial diversity was observed in a sample made with a starter culture from pasteurised milk. Metagenomic analysis by high-throughput sequencing using 16S rRNA genes seems to be a powerful tool for studying the structure of the microbial population in cheeses.

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Metagenomic De Novo Assembly of an Aquatic Representative of the Verrucomicrobial Class Spartobacteria

mBio ◽

10.1128/mbio.00569-12 ◽

2013 ◽

Vol 4 (3) ◽

Cited By ~ 64

Author(s):

Daniel P. R. Herlemann ◽

Daniel Lundin ◽

Matthias Labrenz ◽

Klaus Jürgens ◽

Zongli Zheng ◽

...

Keyword(s):

16S Rrna ◽

Carbon Cycle ◽

Baltic Sea ◽

Glycoside Hydrolases ◽

16S Rrna Genes ◽

Rrna Genes ◽

Sulfated Polysaccharides ◽

The Baltic Sea ◽

The Baltic

ABSTRACTThe verrucomicrobial subdivision 2 classSpartobacteriais one of the most abundant bacterial lineages in soil and has recently also been found to be ubiquitous in aquatic environments. A 16S rRNA gene study from samples spanning the entire salinity range of the Baltic Sea indicated that, in the pelagic brackish water, a phylotype of theSpartobacteriais one of the dominating bacteria during summer. Phylogenetic analyses of related 16S rRNA genes indicate that a purely aquatic lineage within theSpartobacteriaexists. Since no aquatic representative from theSpartobacteriahas been cultured or sequenced, the metabolic capacity and ecological role of this lineage are yet unknown. In this study, we reconstructed the genome and metabolic potential of the abundant Baltic SeaSpartobacteriaphylotype by metagenomics. Binning of genome fragments by nucleotide composition and a self-organizing map recovered the near-complete genome of the organism, the gene content of which suggests an aerobic heterotrophic metabolism. Notably, we found 23 glycoside hydrolases that likely allow the use of a variety of carbohydrates, like cellulose, mannan, xylan, chitin, and starch, as carbon sources. In addition, a complete pathway for sulfate utilization was found, indicating catabolic processing of sulfated polysaccharides, commonly found in aquatic phytoplankton. The high frequency of glycoside hydrolase genes implies an important role of this organism in the aquatic carbon cycle. Spatiotemporal data of the phylotype’s distribution within the Baltic Sea indicate a connection toCyanobacteriathat may be the main source of the polysaccharide substrates.IMPORTANCEThe ecosystem roles of many phylogenetic lineages are not yet well understood. One such lineage is the classSpartobacteriawithin theVerrucomicrobiathat, despite being abundant in soil and aquatic systems, is relatively poorly studied. Here we circumvented the difficulties of growing aquaticVerrucomicrobiaby applying shotgun metagenomic sequencing on a water sample from the Baltic Sea. By using a method based on sequence signatures, we were able toin silicoisolate genome fragments belonging to a phylotype of theSpartobacteria. The genome, which represents the first aquatic representative of this clade, encodes a diversity of glycoside hydrolases that likely allow degradation of various complex carbohydrates. Since the phylotype cooccurs withCyanobacteria, these may be the primary producers of the carbohydrate substrates. The phylotype, which is highly abundant in the Baltic Sea during summer, may thus play an important role in the carbon cycle of this ecosystem.

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Analysis of Bacterial Activity in Sound and Cariogenic Biofilm: A Pilot in vivo Study

Caries Research ◽

10.1159/000448485 ◽

2016 ◽

Vol 50 (5) ◽

pp. 480-488 ◽

Cited By ~ 11

Author(s):

Karsten Henne ◽

Antonia-Patricia Gunesch ◽

Carolin Walther ◽

Hendrik Meyer-Lueckel ◽

Georg Conrads ◽

...

Keyword(s):

16S Rrna ◽

Activity Patterns ◽

Donor Site ◽

Relative Activity ◽

16S Rrna Genes ◽

Rrna Genes ◽

Associated Bacteria ◽

Caries Lesions ◽

Plaque Biofilm

Dental caries is a multifactorial disease with many associated microbial taxa, but only a few are notably contributing to acidogenicity. The ribosome number and the corresponding 16S ribosomal RNA (rRNA) concentration are considered a molecular indicator for general metabolic activity of bacteria, as they are elevated with increased anabolic and catabolic activities. We hypothesize that the activity of aciduric/acidogenic bacterial taxa, reflected by a rise in ribosomal counts, could resolve differences between plaque biofilm from sound surfaces and caries lesions. The included subjects were allocated to two groups: caries-free (CF) or caries-active (CA). CF subjects presented one donor site, namely one sound surface (CFS, n = 10), whereas CA subjects presented two donor sites: a cavitated lesion with an ICDAS score of 5-6 (CAC, n = 13), and a sound reference surface (CAS, n = 13). Four aciduric/acidogenic bacterial taxa (Streptococcus mutans, lactobacilli, Bifidobacterium dentium, and Scardovia wiggsiae) and one asaccharolytic taxon (fusobacteria) as a contrast were selected. 16S rRNA and 16S rRNA genes were quantified by quantitative PCR. Based on these parameters, bacterial and ribosomal counts, as well as relative activities were calculated as the quotient of relative ribosomal abundance and relative genome abundance. Caries-associated bacteria showed the highest relative activity in caries lesions (e.g. lactobacilli CAC: 177.5 ± 46.0%) and lower activities on sound surfaces (e.g. lactobacilli CAS: 96.3 ± 31.5%), whereas asaccharolytic fusobacteria were most active on sound surfaces and less active in caries lesions (CFS: 275.7 ± 171.1%; CAS: 205.8 ± 114.3%; CAC: 51.1 ± 19.0%). Thus, the present study suggests different activity patterns for biofilms from CF and CA individuals.

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Natural Niche for Organohalide-Respiring Chloroflexi

Applied and Environmental Microbiology ◽

10.1128/aem.06510-11 ◽

2011 ◽

Vol 78 (2) ◽

pp. 393-401 ◽

Cited By ~ 102

Author(s):

Mark J. Krzmarzick ◽

Benjamin B. Crary ◽

Jevon J. Harding ◽

Oyenike O. Oyerinde ◽

Alessandra C. Leri ◽

...

Keyword(s):

16S Rrna ◽

Terrestrial Ecosystems ◽

16S Rrna Genes ◽

Rrna Genes ◽

Soil Core ◽

Content Type ◽

Integral Role ◽

Terrestrial Environments ◽

Inorganic Chloride

ABSTRACTThe phylumChloroflexicontains several isolated bacteria that have been found to respire a diverse array of halogenated anthropogenic chemicals. The distribution and role of theseChloroflexiin uncontaminated terrestrial environments, where abundant natural organohalogens could function as potential electron acceptors, have not been studied. Soil samples (116 total, including 6 sectioned cores) from a range of uncontaminated sites were analyzed for the number ofDehalococcoides-likeChloroflexi16S rRNA genes present.Dehalococcoides-likeChloroflexipopulations were detected in all but 13 samples. The concentrations of organochlorine ([organochlorine]), inorganic chloride, and total organic carbon (TOC) were obtained for 67 soil core sections. The number ofDehalococcoides-likeChloroflexi16S rRNA genes positively correlated with [organochlorine]/TOC while the number ofBacteria16S rRNA genes did not.Dehalococcoides-likeChloroflexiwere also observed to increase in number with a concomitant accumulation of chloride when cultured with an enzymatically produced mixture of organochlorines. This research provides evidence that organohalide-respiringChloroflexiare widely distributed as part of uncontaminated terrestrial ecosystems, they are correlated with the fraction of TOC present as organochlorines, and they increase in abundance while dechlorinating organochlorines. These findings suggest that organohalide-respiringChlorofleximay play an integral role in the biogeochemical chlorine cycle.

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Cross-Shore and Depth Zonations in Bacterial Diversity Are Linked to Age and Source of Dissolved Organic Matter across the Intertidal Area of a Sandy Beach

Microorganisms ◽

10.3390/microorganisms9081720 ◽

2021 ◽

Vol 9 (8) ◽

pp. 1720

Author(s):

Julius Degenhardt ◽

Julian Merder ◽

Benedikt Heyerhoff ◽

Heike Simon ◽

Bert Engelen ◽

...

Keyword(s):

Organic Matter ◽

Dissolved Organic Matter ◽

16S Rrna Genes ◽

Rrna Genes ◽

Ion Cyclotron Resonance ◽

Reactive Iron ◽

Metabolic Functions ◽

Beach Sediments ◽

Ft Icr Ms

Microbial communities and dissolved organic matter (DOM) are intrinsically linked within the global carbon cycle. Demonstrating this link on a molecular level is hampered by the complexity of both counterparts. We have now investigated this connection within intertidal beach sediments, characterized by a runnel-ridge system and subterranean groundwater discharge. Using datasets generated by Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) and Ilumina-sequencing of 16S rRNA genes, we predicted metabolic functions and determined links between bacterial communities and DOM composition. Four bacterial clusters were defined, reflecting differences within the community compositions. Those were attributed to distinct areas, depths, or metabolic niches. Cluster I was found throughout all surface sediments, probably involved in algal-polymer degradation. In ridge and low water line samples, cluster III became prominent. Associated porewaters indicated an influence of terrestrial DOM and the release of aromatic compounds from reactive iron oxides. Cluster IV showed the highest seasonality and was associated with species previously reported from a subsurface bloom. Interestingly, Cluster II harbored several members of the candidate phyla radiation (CPR) and was related to highly degraded DOM. This may be one of the first geochemical proofs for the role of candidate phyla in the degradation of highly refractory DOM.

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