A dual sequence and culture-based survey of maize rhizosphere protists reveals dominant, plant-enriched, and culturable community members

Protists play important roles in shaping the microbial community of the rhizosphere. However, there is still a limited understanding of how plants shape the protist community, and how well protist isolate collections might represent rhizosphere protist composition and function in downstream studies. We sought to determine whether maize roots select for a distinct protist community in the field, and whether the common or dominant members of that community are readily culturable using standard protist isolation methods. We sequenced 18S and 16S rRNA genes from the rhizospheres of maize grown in two sites, and isolated 103 protists into culture from the same roots. While field site had the greatest effect, rhizospheres in both sites had distinct protist composition from the bulk soils, and certain taxa were enriched in both sites. Enriched taxa were correlated to bacterial abundance patterns. The isolated protists represented six supergroups, and the majority corresponded to taxa found in the sequencing survey. Twenty-six isolates matched eight of the 89 core rhizosphere taxa. This study demonstrates that maize roots select for a distinct protist community, but also illustrate the potential challenges in understanding the function of the dominant protist groups in the rhizosphere.

Download Full-text

Bacterial Diversity and Function of Aerobic Granules Engineered in a Sequencing Batch Reactor for Phenol Degradation

Applied and Environmental Microbiology ◽

10.1128/aem.70.11.6767-6775.2004 ◽

2004 ◽

Vol 70 (11) ◽

pp. 6767-6775 ◽

Cited By ~ 98

Author(s):

He-Long Jiang ◽

Joo-Hwa Tay ◽

Abdul Majid Maszenan ◽

Stephen Tiong-Lee Tay

Keyword(s):

Microbial Community ◽

16S Rrna ◽

Bacterial Diversity ◽

Sequencing Batch Reactor ◽

Batch Reactor ◽

Phenol Degradation ◽

16S Rrna Genes ◽

Rrna Genes ◽

Aerobic Granules ◽

And Function

ABSTRACT Aerobic granules are self-immobilized aggregates of microorganisms and represent a relatively new form of cell immobilization developed for biological wastewater treatment. In this study, both culture-based and culture-independent techniques were used to investigate the bacterial diversity and function in aerobic phenol- degrading granules cultivated in a sequencing batch reactor. Denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified 16S rRNA genes demonstrated a major shift in the microbial community as the seed sludge developed into granules. Culture isolation and DGGE assays confirmed the dominance of β-Proteobacteria and high-G+C gram-positive bacteria in the phenol-degrading aerobic granules. Of the 10 phenol-degrading bacterial strains isolated from the granules, strains PG-01, PG-02, and PG-08 possessed 16S rRNA gene sequences that matched the partial sequences of dominant bands in the DGGE fingerprint belonging to the aerobic granules. The numerical dominance of strain PG-01 was confirmed by isolation, DGGE, and in situ hybridization with a strain-specific probe, and key physiological traits possessed by PG-01 that allowed it to outcompete and dominate other microorganisms within the granules were then identified. This strain could be regarded as a functionally dominant strain and may have contributed significantly to phenol degradation in the granules. On the other hand, strain PG-08 had low specific growth rate and low phenol degradation ability but showed a high propensity to autoaggregate. By analyzing the roles played by these two isolates within the aerobic granules, a functional model of the microbial community within the aerobic granules was proposed. This model has important implications for rationalizing the engineering of ecological systems.

Download Full-text

Dix-seq: An integrated pipeline for fast amplicon data analysis

10.1101/2020.05.11.089748 ◽

2020 ◽

Author(s):

Yongjun wei ◽

Tianqi Ren ◽

Lei Zhang

Keyword(s):

Sequence Data ◽

Gene Diversity ◽

16S Rrna Genes ◽

Rrna Genes ◽

Sequencing Technologies ◽

Functional Gene Diversity ◽

Internal Transcribed Spacer Sequences ◽

The Common ◽

18S Rrna Genes ◽

Multiple Samples

AbstractThe amplicon derived from 16S rRNA genes, 18S rRNA genes, internal transcribed spacer sequences or other functional genes can be used to infer and evaluate microbial diversity or functional gene diversity. With the development of sequencing technologies, large amounts of amplicon data were generated. Several different software or pipelines had been developed for amplicon data analyses. However, most current software/pipelines require multistep and advanced programming skills. Moreover, they are often complex and time-consuming. Here, we introduced an integrated pipeline named Dix-seq for high-throughput amplicon sequence data processing (https://github.com/jameslz/dix-seq). Dix-seq integrates several different amplicon analysis algorithms and software for diversity analyses of multiple samples. Dix-seq analyzes amplicon sequences efficiently, and exports abundant visual results automatically with only one command in Linux environment. In summary, Dix-seq enables the common/advanced users to generate amplicon analysis results easily and offers a versatile and convenient tool for researchers.

Download Full-text

Phylogenetic Evidence for the Existence of Novel Thermophilic Bacteria in Hot Spring Sulfur-Turf Microbial Mats in Japan

Applied and Environmental Microbiology ◽

10.1128/aem.64.5.1680-1687.1998 ◽

1998 ◽

Vol 64 (5) ◽

pp. 1680-1687 ◽

Cited By ~ 78

Author(s):

Hiroyuki Yamamoto ◽

Akira Hiraishi ◽

Kenji Kato ◽

Hiroshi X. Chiura ◽

Yonosuke Maki ◽

...

Keyword(s):

16S Rrna ◽

Microbial Mats ◽

Hot Springs ◽

Hot Spring ◽

Thermophilic Bacteria ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rdna Sequences ◽

Major Cluster ◽

The Common

ABSTRACT So-called sulfur-turf microbial mats, which are macroscopic white filaments or bundles consisting of large sausage-shaped bacteria and elemental sulfur particles, occur in sulfide-containing hot springs in Japan. However, no thermophiles from sulfur-turf mats have yet been isolated as cultivable strains. This study was undertaken to determine the phylogenetic positions of the sausage-shaped bacteria in sulfur-turf mats by direct cloning and sequencing of 16S rRNA genes amplified from the bulk DNAs of the mats. Common clones with 16S rDNA sequences with similarity levels of 94.8 to 99% were isolated from sulfur-turf mat samples from two geographically remote hot springs. Phylogenetic analysis showed that the phylotypes of the common clones formed a major cluster with members of theAquifex-Hydrogenobacter complex, which represents the most deeply branching lineage of the domain bacteria. Furthermore, the bacteria of the sulfur-turf mat phylotypes formed a clade distinguishable from that of other members of theAquifex-Hydrogenobacter complex at the order or subclass level. In situ hybridization with clone-specific probes for 16S rRNA revealed that the common phylotype of sulfur-turf mat bacteria is that of the predominant sausage-shaped bacteria.

Download Full-text

Vegetation-Dependent Response to Drought in Salt Marsh Ammonia-Oxidizer Communities

Microorganisms ◽

10.3390/microorganisms8010009 ◽

2019 ◽

Vol 8 (1) ◽

pp. 9

Author(s):

Jack K. Beltz ◽

Hayley McMahon ◽

Isis Torres Nunez ◽

Anne E. Bernhard

Keyword(s):

Salt Marsh ◽

Community Composition ◽

Bacterial Abundance ◽

16S Rrna Genes ◽

Rrna Genes ◽

Ammonia Oxidizer ◽

N Availability ◽

Ammonia Oxidizing Archaea ◽

Vegetation Zones ◽

Total Bacterial Community

We investigated the impacts of drought on ammonia-oxidizing archaea (AOA) and bacteria (AOB) in a salt marsh and compared the response to the total bacterial community. We analyzed abundance and community composition of amoA genes by QPCR and TRFLP, respectively, in three vegetation zones in 2014 (pre-drought), 2016 (drought), and 2017 (post-drought), and analyzed bacterial 16S rRNA genes by QPCR, TRFLP, and MiSeq analyses. AOA and AOB abundance in the Spartina patens zone increased significantly in 2016, while abundance decreased in the tall S. alterniflora zone, and showed little change in the short S. alterniflora zone. Total bacterial abundance declined annually in all vegetation zones. Significant shifts in community composition were detected in 2016 in two of the three vegetation zones for AOA and AOB, and in all three vegetation zones for total bacteria. Abundance and community composition of AOA and AOB returned to pre-drought conditions by 2017, while bacterial abundance continued to decline, suggesting that nitrifiers may be more resilient to drought than other bacterial communities. Finding vegetation-specific drought responses among N-cycling microbes may have broad implications for changes in N availability and marsh productivity, particularly if vegetation patterns continue to shift as predicted due to sea level rise.

Download Full-text

Effects of Agronomic Treatments on Structure and Function of Ammonia-Oxidizing Communities

Applied and Environmental Microbiology ◽

10.1128/aem.66.12.5410-5418.2000 ◽

2000 ◽

Vol 66 (12) ◽

pp. 5410-5418 ◽

Cited By ~ 141

Author(s):

Carol J. Phillips ◽

Dave Harris ◽

Sherry L. Dollhopf ◽

Katherine L. Gross ◽

James I. Prosser ◽

...

Keyword(s):

Denaturing Gradient Gel Electrophoresis ◽

Deciduous Forest ◽

16S Rrna Genes ◽

Rrna Genes ◽

Ammonia Oxidizer ◽

Most Probable Number ◽

Ammonia Oxidizers ◽

Probable Number ◽

Gradient Gel Electrophoresis ◽

And Function

ABSTRACT The aim of this study was to determine the effects of different agricultural treatments and plant communities on the diversity of ammonia oxidizer populations in soil. Denaturing gradient gel electrophoresis (DGGE), coupled with specific oligonucleotide probing, was used to analyze 16S rRNA genes of ammonia oxidizers belonging to the β subgroup of the division Proteobacteria by use of DNA extracted from cultivated, successional, and native deciduous forest soils. Community profiles of the different soil types were compared with nitrification rates and most-probable-number (MPN) counts. Despite significant variation in measured nitrification rates among communities, there were no differences in the DGGE banding profiles of DNAs extracted from these soils. DGGE profiles of DNA extracted from samples of MPN incubations, cultivated at a range of ammonia concentrations, showed the presence of bands not amplified from directly extracted DNA. Nitrosomonas-like bands were seen in the MPN DNA but were not detected in the DNA extracted directly from soils. These bands were detected in some samples taken from MPN incubations carried out with medium containing 1,000 μg of NH4 +-N ml−1, to the exclusion of bands detected in the native DNA. Cell concentrations of ammonia oxidizers determined by MPN counts were between 10- and 100-fold lower than those determined by competitive PCR (cPCR). Although no differences were seen in ammonia oxidizer MPN counts from the different soil treatments, cPCR revealed higher numbers in fertilized soils. The use of a combination of traditional and molecular methods to investigate the activities and compositions of ammonia oxidizers in soil demonstrates differences in fine-scale compositions among treatments that may be associated with changes in population size and function.

Download Full-text

AB0824 ANALYSIS OF GUT MICROBIOTA IN RHEUMATOID ARTHRITIS PATIENTS

Annals of the Rheumatic Diseases ◽

10.1136/annrheumdis-2021-eular.1944 ◽

2021 ◽

Vol 80 (Suppl 1) ◽

pp. 1436.1-1436

Author(s):

Q. Wang ◽

S. X. Zhang ◽

J. Qiao ◽

G. Shi ◽

R. Zhao ◽

...

Keyword(s):

Rheumatoid Arthritis ◽

Gut Microbiota ◽

Intestinal Flora ◽

16S Rrna Genes ◽

Rrna Genes ◽

Shanxi Province ◽

Gastrointestinal Microbiota ◽

Hematopoietic Stem ◽

Variable Regions ◽

And Function

Background:Gastrointestinal microbiota, particularly gut microbiota is an indispensable environmental factor in the progression of Rheumatoid Arthritis (RA). Understanding the diversity and function of the intestinal flora in patients with RA is part and parcel to understand the relationship between microbiota and human health.Objectives:This study aimed to identify the diversity and function of the intestinal flora in patients with RA.Methods:A total of 166 participants were recruited in this study, comprising 93 RA patients and 73 age and sex-matched healthy controls (HCs). Microbial genome was extracted from approximately 250mg fresh fecal samples from all participants using QIAamp PowerFecal DNA Kit (Qiagen). The V3-V4 variable regions of bacterial 16S rRNA genes were sequenced with the Illumina Miseq PE300 system. Sequence data were compiled and processed using Qiime2. Sequences were grouped into operational taxonomic units (ASVs)1. Microbial diversity was estimated by the Simpson index. PICRUSt2 was used to predict KEGG functional pathway differences between RA and HC intestinal flora functions based on ASV Tables2. Linear Discriminant Analysis (LDA) Effect Size (LEfSe) analysis was performed using LEfSe software to discovery the different intestinal flora and functions between RA and healthy.Results:The alpha-diversity index of Simpson the microbiome in RA patients was lower than that of HCs (Figure 1a, P <0.05). Compared with HCs, bacterial Bacilli and Lactobacillales were more abundant in patients with RA (Figure 1b, P <0.05). In contrast, Marinifilaceae, Peptococcaceae, Peptococcales and Phascolarcto bacterium were less abundant in the RA group (Figure 1b, P <0.05). As shown in Figure 1c, propanoate metabolism, taurine and hypotaurine metabolism, ascorbate and aldarate metabolism, biosynthesis of siderophore group nonribosomal peptides and glutathione metabolism were the most significantly altered pathways in RA (P <0.05). Epithelial cell signaling in Helicobacter pylori infection, RNA transport, RNA degradation and plant-pathogen interaction were the most significantly altered pathways in HC (P <0.05). The different KEGG metabolic pathways were mainly concentrated in carbohydrate and amino acid metabolism.Conclusion:Gut dysbiosis in RA patients mainly characterized by reduced the diversity and impaired abundance of the intestinal flora, which severely influence the metabolism of gastrointestinal microbiota. The discovery of the associated intestinal microbiota of RA may provide a new idea for RA treatment.References:[1]Han L, Zhao K, Li Y, et al. A gut microbiota score predicting acute graft-versus-host disease following myeloablative allogeneic hematopoietic stem cell transplantation. Am J Transplant 2020;20(4):1014-27. doi: 10.1111/ajt.15654 [published Online First: 2019/10/13][2]Liss MA, White JR, Goros M, et al. Metabolic Biosynthesis Pathways Identified from Fecal Microbiome Associated with Prostate Cancer. Eur Urol 2018;74(5):575-82. doi: 10.1016/j.eururo.2018.06.033 [published Online First: 2018/07/17]Acknowledgements:This project was supported by National Science Foundation of China (82001740), Open Fund from the Key Laboratory of Cellular Physiology (Shanxi Medical University) (KLCP2019) and Innovation Plan for Postgraduate Education in Shanxi Province (2020BY078).Disclosure of Interests:None declared

Download Full-text

Resuscitation of soil microbiota after > 70-years of desiccation

10.1101/2020.11.06.371641 ◽

2020 ◽

Author(s):

Jun Zhao ◽

Dongfeng Chen ◽

Wei Gao ◽

Zhiying Guo ◽

Zhongjun Jia ◽

...

Keyword(s):

High Throughput Sequencing ◽

Bacterial Abundance ◽

Storage Conditions ◽

16S Rrna Genes ◽

Rrna Genes ◽

Sequencing Analysis ◽

Osmotic Change ◽

Abundance And Diversity ◽

Strong Adaptation

AbstractThe abundance and diversity of bacteria in 24 historical soil samples under air-dried storage conditions for more than 70 years were assessed by quantification and high-throughput sequencing analysis of 16S rRNA genes. All soils contained a measurable abundance of bacteria varying from 103 to 108 per gram of soil and contrasting community compositions were observed in different background soils, suggesting that the bacteria detected were indigenous to the soil. Following a 4-week soil rewetting event, the bacterial abundance significantly increased in soils, indicating strong adaptation of soil bacteria to extreme osmotic change and high resuscitation potential of some bacteria over long periods of desiccation. Paenibacillus, Cohnella and two unclassified Bacillales genera within the phylum Firmicutes represented the most ubiquitously active taxa, which showed growth in the highest number of soils (≥12 soils), while genera Tumebacillus, Alicyclobacillus and Brevibacillus in the phylum Firmicutes displayed the highest growth rates in soils (with >1000-fold average increase) following rewetting. Additionally, some Actinobacteria and Proteobacteria genera showed relatively high activity following rewetting, suggesting that the resilience to long-term desiccation and rewetting is a common trait across phylogenetically divergent microbes. The present study thus demonstrated that diversified groups of microbes are present and potentially active in historically desiccated soils, which might be of importance in the context of microbial ecology.

Download Full-text

The Problem with ‘Microbiome’

Diversity ◽

10.3390/d13040138 ◽

2021 ◽

Vol 13 (4) ◽

pp. 138

Author(s):

Stuart Donachie ◽

Claire Fraser ◽

Ethan Hill ◽

Marguerite Butler

Keyword(s):

16S Rrna ◽

Microbial Diversity ◽

Sensu Stricto ◽

Ribosomal Gene ◽

16S Rrna Genes ◽

Rrna Genes ◽

Community Members ◽

Etiologic Agents ◽

Microbiome Research ◽

Marine Microbial Diversity

The term “microbiome” is currently applied predominantly to assemblages of organisms with 16S rRNA genes. In this context, “microbiome” is a misnomer that has been conferred a wide-ranging primacy over terms for community members lacking such genes, e.g., mycobiome, eukaryome, and virome, yet these are also important subsets of microbial communities. Widespread convenient and affordable 16S rRNA sequencing pipelines have accelerated continued use of such a “microbiome”, but at what intellectual and practical costs? Here we show that the use of “microbiome” in ribosomal gene-based studies has been egregiously misapplied, and discuss potential impacts. We argue that the current focus of “microbiome” research, predominantly on only ‘bacteria’, presents a dangerous narrowing of scope which encourages dismissal and even ignorance of other organisms’ contributions to microbial diversity, sensu stricto, and as etiologic agents; we put this in context by discussing cases in both marine microbial diversity and the role of pathogens in global amphibian decline. Fortunately, the solution is simple. We must use descriptive nouns that strictly reflect the outcomes attainable by the methods used. “Microbiome”, as a descriptive noun, should only be used when diversity in the three recognized domains is explored.

Download Full-text

RNA–Stable-Isotope Probing Shows Utilization of Carbon from Inulin by Specific Bacterial Populations in the Rat Large Bowel

Applied and Environmental Microbiology ◽

10.1128/aem.03799-13 ◽

2014 ◽

Vol 80 (7) ◽

pp. 2240-2247 ◽

Cited By ~ 28

Author(s):

Gerald W. Tannock ◽

Blair Lawley ◽

Karen Munro ◽

Ian M. Sims ◽

Julian Lee ◽

...

Keyword(s):

Stable Isotope ◽

Bacterial Species ◽

Buoyant Density ◽

Stable Isotope Probing ◽

16S Rrna Genes ◽

Rrna Genes ◽

Bacterial Cells ◽

Bacterial Populations ◽

Content Type ◽

And Function

ABSTRACTKnowledge of the trophisms that underpin bowel microbiota composition is required in order to understand its complex phylogeny and function. Stable-isotope (13C)-labeled inulin was added to the diet of rats on a single occasion in order to detect utilization of inulin-derived substrates by particular members of the cecal microbiota. Cecal digesta from Fibruline-inulin-fed rats was collected prior to (0 h) and at 6, 12, 18 and 24 h following provision of the [13C]inulin diet. RNA was extracted from these cecal specimens and fractionated in isopycnic buoyant density gradients in order to detect13C-labeled nucleic acid originating in bacterial cells that had metabolized the labeled dietary constituent. RNA extracted from specimens collected after provision of the labeled diet was more dense than 0-h RNA. Sequencing of 16S rRNA genes amplified from cDNA obtained from these fractions showed thatBacteroides uniformis,Blautia glucerasea,Clostridium indolis, andBifidobacterium animaliswere the main users of the13C-labeled substrate. Culture-based studies of strains of these bacterial species enabled trophisms associated with inulin and its hydrolysis products to be identified.B. uniformisutilized Fibruline-inulin for growth, whereas the other species used fructo-oligosaccharide and monosaccharides. Thus, RNA–stable-isotope probing (RNA-SIP) provided new information about the use of carbon from inulin in microbiota metabolism.

Download Full-text

Iron Flocs and the Three Domains: Microbial Interactions in Freshwater Iron Mats

mBio ◽

10.1128/mbio.02720-20 ◽

2020 ◽

Vol 11 (6) ◽

pp. e02720-20

Author(s):

Chequita N. Brooks ◽

Erin K. Field

Keyword(s):

Functional Groups ◽

Keystone Species ◽

Microbial Interactions ◽

16S Rrna Genes ◽

Rrna Genes ◽

Community Members ◽

Holistic View ◽

Iron Oxidizing Bacteria ◽

Pollution Removal ◽

Laboratory Culturing

ABSTRACTFreshwater iron mats are dynamic geochemical environments with broad ecological diversity, primarily formed by the iron-oxidizing bacteria. The community features functional groups involved in biogeochemical cycles for iron, sulfur, carbon, and nitrogen. Despite this complexity, iron mat communities provide an excellent model system for exploring microbial ecological interactions and ecological theories in situ. Syntrophies and competition between the functional groups in iron mats, how they connect cycles, and the maintenance of these communities by taxons outside bacteria (the eukaryota, archaea, and viruses) have been largely unstudied. Here, we review what is currently known about freshwater iron mat communities, the taxa that reside there, and the interactions between these organisms, and we propose ways in which future studies may uncover exciting new discoveries. For example, the archaea in these mats may play a greater role than previously thought as they are diverse and widespread in iron mats based on 16S rRNA genes and include methanogenic taxa. Studies with a holistic view of the iron mat community members focusing on their diverse interactions will expand our understanding of community functions, such as those involved in pollution removal. To begin addressing questions regarding the fundamental interactions and to identify the conditions in which they occur, more laboratory culturing techniques and coculture studies, more network and keystone species analyses, and the expansion of studies to more freshwater iron mat systems are necessary. Increasingly accessible bioinformatic, geochemical, and culturing tools now open avenues to address the questions that we pose herein.

Download Full-text