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

mBio ◽  
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.

Molecular Identification of Iron Oxidizing Bacteria Isolated from Acid Mine Drainages in Peru

2013 ◽  
Vol 825 ◽  
pp. 84-87 ◽  
Author(s):  
Michel Abanto ◽  
Nicolaza Pariona ◽  
Julio Calderon ◽  
Gregory Guerra ◽  
Rina Ramirez ◽  
...  
Keyword(s):  
Acid Mine Drainage ◽  
16S Rrna ◽  
Mine Drainage ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Acid Mine ◽  
The North ◽  
Acidophilic Bacteria ◽  
Iron Oxidizing Bacteria ◽  
Acid Mine Drainage Generation

Acidophilic iron-oxidizing microorganisms are important in both environmental and biotechnological applications. These microorganisms are known to accelerate the dissolution of sulfur minerals such as pyrite (FeS2), leading to the acid mine drainage generation , a serious pollution problem, that makes these microorganisms essential to the commercial processing of minerals and sulfur. In order to answer this question, diversity of native acidophilic bacteria isolated from acid mine drainage of Peru was evaluated. The samples were collected from Yanacocha mining (3000 m.a.s.l.) located in the North of Cajamarca region, Yanamina mining (4440 m.a.s.l.) located in the middle of Huancavelica region; finally, SPCC mining (2000 m.a.s.l.) located in the South of Moquegua region. We isolated 11 strains from which three were identified asAcidithiobacillus ferrooxidans, two asAt. ferrivorans, two asAt. ferridurans,three asLeptospirillum ferrooxidansand one asAcidiphilium sp.by comparative sequencing of PCR-amplified 16S rRNA genes. Phylogenetic analysis of the 16S rRNA genes revealed that some of the strains isolated are closely related to other already known, but there are some with similarities lower than < 95 percent. Our results provide the first study on the diversity of iron-oxidizing bacteria isolated from acid mine drainage of Peru.

scholarly journals Native and invading yellow starthistle (Centaurea solstitialis) microbiomes differ in composition and diversity of bacteria

2017 ◽  
Author(s):  
Patricia Lu-Irving ◽  
Julia Harenčár ◽  
Hailey Sounart ◽  
Shana R Welles ◽  
Sarah M Swope ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Plant Pathogens ◽  
Bacterial Community Composition ◽  
Microbial Interactions ◽  
Invasion Success ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
List Type ◽  
Plant Genotype ◽  
Yellow Starthistle

SUMMARYInvasive species could benefit from introduction to locations with favorable species interactions. Microbiomes are an important source of interactions that vary across regions. We examine whether bacterial communities could explain more favorable microbial interactions in highly invasive populations of yellow starthistle.We sequenced amplicons of prokaryotic 16S rRNA genes to characterize bacterial community composition in the phyllosphere, ectorhizosphere, and endorhizosphere of plants from seven invading populations in California, USA and eight native populations in Europe. We tested for differentiation of microbiomes by geography, plant compartment, and plant genotype.Bacterial communities differed significantly between native and invaded ranges within plant compartments, with consistently lower diversity in plants from the invaded range. Genera containing known plant pathogens also showed lower diversity in invaded range plants. The diversity of bacteria in roots was positively correlated with plant genotype diversity within both ranges, but this relationship did not explain microbial differences between ranges.Our findings reveal changes in the composition and diversity of bacterial interactions in invading plants, consistent with observations of altered soil interactions in this invasion. These results call for further study of the sources of variation in microbiomes and the potential for bacteria to facilitate invasion success.

scholarly journals Native and Invading Yellow Starthistle (Centaurea solstitialis) Microbiomes Differ in Composition and Diversity of Bacteria

mSphere ◽  
2019 ◽  
Vol 4 (2) ◽  
Author(s):  
Patricia Lu-Irving ◽  
Julia G. Harenčár ◽  
Hailey Sounart ◽  
Shana R. Welles ◽  
Sarah M. Swope ◽  
...  
Keyword(s):  
Species Interactions ◽  
Invasive Plant ◽  
Microbial Interactions ◽  
Invasion Success ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Centaurea Solstitialis ◽  
Plant Genotype ◽  
Yellow Starthistle ◽  
Content Type

ABSTRACTInvasive species could benefit from being introduced to locations with more favorable species interactions, including the loss of enemies, the gain of mutualists, or the simplification of complex interaction networks. Microbiomes are an important source of species interactions with strong fitness effects on multicellular organisms, and these interactions are known to vary across regions. The highly invasive plant yellow starthistle (Centaurea solstitialis) has been shown to experience more favorable microbial interactions in its invasions of the Americas, but the microbiome that must contribute to this variation in interactions is unknown. We sequenced amplicons of 16S rRNA genes to characterize bacterial community compositions in the phyllosphere, ectorhizosphere, and endorhizosphere of yellow starthistle plants from seven invading populations in California, USA, and eight native populations in Europe. We tested for the differentiation of microbiomes by geography, plant compartment, and plant genotype. Bacterial communities differed significantly between native and invading plants within plant compartments, with consistently lower diversity in the microbiome of invading plants. The diversity of bacteria in roots was positively correlated with plant genotype diversity within both ranges, but this relationship did not explain microbiome differences between ranges. Our results reveal that these invading plants are experiencing either a simplified microbial environment or simplified microbial interactions as a result of the dominance of a few taxa within their microbiome. Our findings highlight several alternative hypotheses for the sources of variation that we observe in invader microbiomes and the potential for altered bacterial interactions to facilitate invasion success.IMPORTANCEPrevious studies have found that introduced plants commonly experience more favorable microbial interactions in their non-native range, suggesting that changes to the microbiome could be an important contributor to invasion success. Little is known about microbiome variation across native and invading populations, however, and the potential sources of more favorable interactions are undescribed. Here, we report one of the first microbiome comparisons of plants from multiple native and invading populations, in the noxious weed yellow starthistle. We identify clear differences in composition and diversity of microbiome bacteria. Our findings raise new questions about the sources of these differences, and we outline the next generation of research that will be required to connect microbiome variation to its potential role in plant invasions.

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

2021 ◽  
Author(s):  
Stephen J Taerum ◽  
Jamie Micciulla ◽  
Gabrielle Corso ◽  
Blaire Steven ◽  
Daniel J. Gage ◽  
...  
Keyword(s):  
Bacterial Abundance ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Field Site ◽  
Community Members ◽  
Abundance Patterns ◽  
Maize Roots ◽  
The Common ◽  
And Function ◽  
Dual Sequence

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.

scholarly journals Lotus japonicus Symbiosis Genes Impact Microbial Interactions between Symbionts and Multikingdom Commensal Communities

mBio ◽  
2019 ◽  
Vol 10 (5) ◽  
Author(s):  
Thorsten Thiergart ◽  
Rafal Zgadzaj ◽  
Zoltán Bozsóki ◽  
Ruben Garrido-Oter ◽  
Simona Radutoiu ◽  
...  
Keyword(s):  
Lotus Japonicus ◽  
Microbial Interactions ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Natural Soil ◽  
Nitrogen Fixing ◽  
Model Legume ◽  
Root Symbionts ◽  
Root Microbiota ◽  
Broad Role

ABSTRACT The wild legume Lotus japonicus engages in mutualistic symbiotic relationships with arbuscular mycorrhiza (AM) fungi and nitrogen-fixing rhizobia. Using plants grown in natural soil and community profiling of bacterial 16S rRNA genes and fungal internal transcribed spacers (ITSs), we examined the role of the Lotus symbiosis genes RAM1, NFR5, SYMRK, and CCaMK in structuring bacterial and fungal root-associated communities. We found host genotype-dependent community shifts in the root and rhizosphere compartments that were mainly confined to bacteria in nfr5 or fungi in ram1 mutants, while symrk and ccamk plants displayed major changes across both microbial kingdoms. We observed in all AM mutant roots an almost complete depletion of a large number of Glomeromycota taxa that was accompanied by a concomitant enrichment of Helotiales and Nectriaceae fungi, suggesting compensatory niche replacement within the fungal community. A subset of Glomeromycota whose colonization is strictly dependent on the common symbiosis pathway was retained in ram1 mutants, indicating that RAM1 is dispensable for intraradical colonization by some Glomeromycota fungi. However, intraradical colonization by bacteria belonging to the Burkholderiaceae and Anaeroplasmataceae is dependent on AM root infection, revealing a microbial interkingdom interaction. Despite the overall robustness of the bacterial root microbiota against major changes in the composition of root-associated fungal assemblages, bacterial and fungal cooccurrence network analysis demonstrates that simultaneous disruption of AM and rhizobium symbiosis increases the connectivity among taxa of the bacterial root microbiota. Our findings imply a broad role for Lotus symbiosis genes in structuring the root microbiota and identify unexpected microbial interkingdom interactions between root symbionts and commensal communities. IMPORTANCE Studies on symbiosis genes in plants typically focus on binary interactions between roots and soilborne nitrogen-fixing rhizobia or mycorrhizal fungi in laboratory environments. We utilized wild type and symbiosis mutants of a model legume, grown in natural soil, in which bacterial, fungal, or both symbioses are impaired to examine potential interactions between the symbionts and commensal microorganisms of the root microbiota when grown in natural soil. This revealed microbial interkingdom interactions between the root symbionts and fungal as well as bacterial commensal communities. Nevertheless, the bacterial root microbiota remains largely robust when fungal symbiosis is impaired. Our work implies a broad role for host symbiosis genes in structuring the root microbiota of legumes.

scholarly journals The Problem with ‘Microbiome’

Diversity ◽  
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.

scholarly journals Seasonal restructuring of the ground squirrel gut microbiota over the annual hibernation cycle

2013 ◽  
Vol 304 (1) ◽  
pp. R33-R42 ◽  
Author(s):  
Hannah V. Carey ◽  
William A. Walters ◽  
Rob Knight
Keyword(s):  
Relative Abundance ◽  
Ground Squirrel ◽  
Phylogenetic Diversity ◽  
Microbial Interactions ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Late Winter ◽  
Maternal Influences ◽  
Operational Taxonomic Units ◽  
Diet History

Many hibernating mammals suspend food intake during winter, relying solely on stored lipids to fuel metabolism. Winter fasting in these species eliminates a major source of degradable substrates to support growth of gut microbes, which may affect microbial community structure and host-microbial interactions. We explored the effect of the annual hibernation cycle on gut microbiotas using deep sequencing of 16S rRNA genes from ground squirrel cecal contents. Squirrel microbiotas were dominated by members of the phyla Bacteroidetes, Firmicutes, and Verrucomicrobia. UniFrac analysis showed that microbiotas clustered strongly by season, and maternal influences, diet history, host age, and host body temperature had minimal effects. Phylogenetic diversity and numbers of operational taxonomic units were lowest in late winter and highest in the spring after a 2-wk period of refeeding. Hibernation increased relative abundance of Bacteroidetes and Verrucomicrobia, phyla that contain species capable of surviving on host-derived substrates such as mucins, and reduced relative abundance of Firmicutes, many of which prefer dietary polysaccharides. Hibernation reduced cecal short-chain fatty acid and ammonia concentrations, and increased and decreased concentrations of acetate and butyrate, respectively. These results indicate that the ground squirrel microbiota is restructured each year in a manner that reflects differences in microbial preferences for dietary vs. host-derived substrates, and thus the competitive abilities of different taxa to survive in the altered environment in the hibernator gut.

scholarly journals Insights into Butyrate Production in a Controlled Fermentation System via Gene Predictions

mSystems ◽  
2017 ◽  
Vol 2 (4) ◽  
Author(s):  
S. Esquivel-Elizondo ◽  
Z. E. Ilhan ◽  
E. I. Garcia-Peña ◽  
R. Krajmalnik-Brown
Keyword(s):  
Fatty Acid ◽  
16S Rrna ◽  
Microbial Interactions ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Functional Prediction ◽  
Fermentation System ◽  
Controlled Systems ◽  
Human Animal ◽  
Butyrate Production

ABSTRACT This study demonstrates how bioinformatics tools, such as metagenome functional prediction from 16S rRNA genes, can help understand biological systems and reveal microbial interactions in controlled systems (e.g., bioreactors). Results obtained from controlled systems are easier to interpret than those from human/animal studies because observed changes may be specifically attributed to the design conditions imposed on the system. Bioinformatics analysis allowed us to identify potential butyrogenic phylotypes and associated butyrate metabolism pathways when we systematically varied the PH2 in a carefully controlled fermentation system. Our insights may be adapted to butyrate production studies in biohydrogen systems and gut models, since butyrate is a main product and a crucial fatty acid in human/animal colon health. Butyrate is a common fatty acid produced in important fermentative systems, such as the human/animal gut and other H2 production systems. Despite its importance, there is little information on the partnerships between butyrate producers and other bacteria. The objective of this work was to uncover butyrate-producing microbial communities and possible metabolic routes in a controlled fermentation system aimed at butyrate production. The butyrogenic reactor was operated at 37°C and pH 5.5 with a hydraulic retention time of 31 h and a low hydrogen partial pressure (PH2). High-throughput sequencing and metagenome functional prediction from 16S rRNA data showed that butyrate production pathways and microbial communities were different during batch (closed) and continuous-mode operation. Lactobacillaceae, Lachnospiraceae, and Enterococcaceae were the most abundant phylotypes in the closed system without PH2 control, whereas Prevotellaceae, Ruminococcaceae, and Actinomycetaceae were the most abundant phylotypes under continuous operation at low PH2. Putative butyrate producers identified in our system were from Prevotellaceae, Clostridiaceae, Ruminococcaceae, and Lactobacillaceae. Metagenome prediction analysis suggests that nonbutyrogenic microorganisms influenced butyrate production by generating butyrate precursors such as acetate, lactate, and succinate. 16S rRNA gene analysis suggested that, in the reactor, a partnership between identified butyrogenic microorganisms and succinate (i.e., Actinomycetaceae), acetate (i.e., Ruminococcaceae and Actinomycetaceae), and lactate producers (i.e., Ruminococcaceae and Lactobacillaceae) took place under continuous-flow operation at low PH2. IMPORTANCE This study demonstrates how bioinformatics tools, such as metagenome functional prediction from 16S rRNA genes, can help understand biological systems and reveal microbial interactions in controlled systems (e.g., bioreactors). Results obtained from controlled systems are easier to interpret than those from human/animal studies because observed changes may be specifically attributed to the design conditions imposed on the system. Bioinformatics analysis allowed us to identify potential butyrogenic phylotypes and associated butyrate metabolism pathways when we systematically varied the PH2 in a carefully controlled fermentation system. Our insights may be adapted to butyrate production studies in biohydrogen systems and gut models, since butyrate is a main product and a crucial fatty acid in human/animal colon health.

scholarly journals Single-Cell Amplicon Sequencing Reveals Community Structures and Transmission Trends of Protist-Associated Bacteria in a Termite Host

2018 ◽  
Author(s):  
Michael E. Stephens ◽  
Daniel J. Gage
Keyword(s):  
Horizontal Transmission ◽  
Amplicon Sequencing ◽  
Reticulitermes Flavipes ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bacterial Symbionts ◽  
Community Members ◽  
Associated Bacteria ◽  
Active Processes ◽  
Protist Species

AbstractThe hindgut protists of wood-feeding termites are usually colonized by prokaryotic symbionts. Many of the hurdles that have prevented a better understanding of these symbionts arise from variation among protist and termite host species and the inability to maintain prominent community members in culture. These issues have made it difficult to study the fidelity, acquisition, and differences in colonization of protists by bacterial symbionts. In this study, we use high throughput amplicon sequencing of the V4 region of 16S rRNA genes to determine the composition of bacterial communities associated with single protist cells of six protist species, from the genera Pyrsonympha, Dinenympha, and Trichonympha that are present in the hindgut of the termite Reticulitermes flavipes. By analyzing amplicon sequence variants (ASVs), the diversity and distribution of protist-associated bacteria was compared within and across these six different protist species. ASV analysis showed that, in general, each protist genus associated with a distinct community of bacterial symbionts which were conserved across different termite colonies. However, some ASVs corresponding to ectosymbionts (Spirochaetes) were shared between different Dinenympha species and to a lesser extent with Pyrsonympha and Trichonympha hosts. This suggested that certain bacterial symbionts may be cosmopolitan to some degree and perhaps acquired by horizontal transmission. Using a fluorescence-based cell assay, we could observe the horizontal acquisition of surface-bound bacteria. This acquisition was shown to be time-dependent, involve active processes, and was non-random with respect to binding locations on some protists.

Differentiation Of Clarias Batrachus, C. Gariepinus And Heteropneustes Fossilis By Pcr-Sequencing Of Mitochondrial 16s Rrna Gene

2015 ◽  
Vol 41 (1) ◽  
pp. 51-58
Author(s):  
Mohammad Shamimul Alam ◽  
Hawa Jahan ◽  
Rowshan Ara Begum ◽  
Reza M Shahjahan
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Fish Larva ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Valuable Insight ◽  
Multiple Sequence ◽  
Pcr Rflp ◽  
Alternative Means

Heteropneustesfossilis, Clariasbatrachus and C. gariepinus are three major catfishes ofecological and economic importance. Identification of these fish species becomes aproblem when the usual external morphological features of the fish are lost or removed,such as in canned fish. Also, newly hatched fish larva is often difficult to identify. PCRsequencingprovides accurate alternative means of identification of individuals at specieslevel. So, 16S rRNA genes of three locally collected catfishes were sequenced after PCRamplification and compared with the same gene sequences available from othergeographical regions. Multiple sequence alignment of the 16S rRNA gene fragments ofthe catfish species has revealed polymorphic sites which can be used to differentiate thesethree species from one another and will provide valuable insight in choosing appropriaterestriction enzymes for PCR-RFLP based identification in future. Asiat. Soc. Bangladesh, Sci. 41(1): 51-58, June 2015

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