Microbiome and Metagenome Analyses of a Closed Habitat during Human Occupation

ABSTRACT Microbial contamination during long-term confinements of space exploration presents potential risks for both crew members and spacecraft life support systems. A novel swab kit was used to sample various surfaces from a submerged, closed, analog habitat to characterize the microbial populations. Samples were collected from various locations across the habitat which were constructed from various surface materials (linoleum, dry wall, particle board, glass, and metal), and microbial populations were examined by culture, quantitative PCR (qPCR), microbiome 16S rRNA gene sequencing, and shotgun metagenomics. Propidium monoazide (PMA)-treated samples identified the viable/intact microbial population of the habitat. The cultivable microbial population ranged from below the detection limit to 106 CFU/sample, and their identity was characterized using Sanger sequencing. Both 16S rRNA amplicon and shotgun sequencing were used to characterize the microbial dynamics, community profiles, and functional attributes (metabolism, virulence, and antimicrobial resistance). The 16S rRNA amplicon sequencing revealed abundance of viable (after PMA treatment) Actinobacteria (Brevibacterium, Nesternkonia, Mycobacterium, Pseudonocardia, and Corynebacterium), Firmicutes (Virgibacillus, Staphylococcus, and Oceanobacillus), and Proteobacteria (especially Acinetobacter) on linoleum, dry wall, and particle board (LDP) surfaces, while members of Firmicutes (Leuconostocaceae) and Proteobacteria (Enterobacteriaceae) were high on the glass/metal surfaces. Nonmetric multidimensional scaling determined from both 16S rRNA and metagenomic analyses revealed differential microbial species on LDP surfaces and glass/metal surfaces. The shotgun metagenomic sequencing of samples after PMA treatment showed bacterial predominance of viable Brevibacterium (53.6%), Brachybacterium (7.8%), Pseudonocardia (9.9%), Mycobacterium (3.7%), and Staphylococcus (2.1%), while fungal analyses revealed Aspergillus and Penicillium dominance. IMPORTANCE This study provides the first assessment of monitoring cultivable and viable microorganisms on surfaces within a submerged, closed, analog habitat. The results of the analyses presented herein suggest that the surface material plays a role in microbial community structure, as the microbial populations differed between LDP and metal/glass surfaces. The metal/glass surfaces had less-complex community, lower bioburden, and more closely resembled the controls. These results indicated that material choice is crucial when building closed habitats, even if they are simply analogs. Finally, while a few species were associated with previously cultivated isolates from the International Space Station and MIR spacecraft, the majority of the microbial ecology of the submerged analog habitat differs greatly from that of previously studied analog habitats.

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Microbiome and Metagenome Analyses of a Closed Habitat During Human Occupation

10.21203/rs.3.rs-21521/v1 ◽

2020 ◽

Author(s):

Ganesh Babu Malli Mohan ◽

Ceth Parker ◽

Camilla Urbaniak ◽

Nitin Singh ◽

Anthony Hood ◽

...

Keyword(s):

16S Rrna ◽

Metal Surfaces ◽

Microbial Population ◽

Microbial Populations ◽

Rrna Gene ◽

Particle Board ◽

Shotgun Metagenomics ◽

Human Habitat ◽

Glass Surfaces ◽

Glass Metal

Abstract Background: Microbial contamination during long-term confinements of space exploration present potential risks for both crew members and spacecraft life support systems. As NASA prepares for manned missions beyond low Earth orbit, deeper into the solar system, the monitoring of microbial populations within closed human habitation will be necessary to ensure the safety of both the crew and the spacecraft. NASA’s Johnson Space Center recently developed a microbial swab kit, designed specifically to be used during astronaut Extravehicular Activity (EVA). The EVA swab kit was designed in such a way that it could be held easily within an astronaut’s bulky glove and or by a robot’s manipulator, making it suitable for microbial sample collection in remote and extreme environments. The previously tested (in laboratory and controlled settings) EVA swab kit was used in this study to sample various surfaces from a submerged, closed, analog habitat in order to characterize the microbial populations in this unique human habitat. Results: Samples were collected from various locations across the habitat of which were constructed from various surface materials (linoleum, dry wall, particle board, glass, and metal) and microbial populations examined by culture, qPCR, microbiome 16S rRNA gene sequencing and shot gun metagenomics. Propidium monoazide treated samples identified the viable/intact microbial population of the habitat. The cultivable microbial population ranged from below the detection limit (BDL) to 10 6 CFU/sample and their identity was characterized using Sanger sequencing. Next-generation sequencing (NGS; both 16S rRNA amplicon and shotgun) were used to characterize the microbial dynamics, community profiles and functional attributes (metabolism, virulence, and antimicrobial resistance). The 16S rRNA amplicon sequencing revealed abundance of viable Actinobacteria ( Brevibacterium , Nesternkonia, Mycobacterium, Pseudonocardia and Corynebacterium ), Firmicutes ( Virgibacillus , Staphylococcus and Oceanobacillus ) and Proteobacteria (esp. Acinetobacter ) on linoleum, dry wall, and particle board (LDP) surfaces, while members of Firmicutes ( Leuconostocaceae ) and Proteobacteria ( Enterobacteriaceae ) were high on the glass/metal surfaces. Non-metric multidimensional scaling (NMDS) determined from both 16S rRNA and metagenomic analyses revealed differential microbial speciation between LDP surfaces and glass/metal surfaces. The shotgun metagenomics sequencing showed bacterial predominance of Brevibacterium (53.6%), Brachybacterium (7.8%), Pseudonocardia (9.9%), Mycobacterium (3.7%), and Staphylococcus (2.1%); while fungal analyses revealed Aspergillus and Penicillium dominance. Conclusion: This study provides the first assessment of monitoring cultivable and viable microorganisms on surfaces within a submerged, closed, analog habitat. The analyses presented herein suggests that the surface material plays a role in microbial community structure as the microbial populations differed between LDP and metal/glass surfaces. The metal/glass surfaces had less complex community, lower bio-burden, and more closely resembled the controls. These results indicated that material choice is crucial when building closed habitats, even if they are simply analogs. Finally, while a few species were associated with previously cultivated isolates from the International Space Station and MIR spacecraft, the majority of the microbial ecology of the submerged Analog habitat differs greatly from that of previously studied analog habitats.

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Microbiome and Metagenome Analyses of a Closed Habitat During Human Occupation

10.21203/rs.2.17229/v1 ◽

2019 ◽

Author(s):

Ganesh Babu Malli Mohan ◽

Ceth W Parker ◽

Camilla Urbaniak ◽

Nitin K Singh ◽

Anthony Drew Hood ◽

...

Keyword(s):

16S Rrna ◽

Microbial Communities ◽

Metal Surfaces ◽

Microbial Population ◽

Life Support ◽

Space Station ◽

Low Earth Orbit ◽

Sample Collection ◽

Glass Surfaces ◽

Glass Metal

Abstract Background: Microbial contamination during the long-term confinements of space exploration present a potential risk for both crew members and spacecraft life support systems. As NASA moves from low Earth orbit further into the solar system, the monitoring of microbial populations within closed human habitation will be necessary to ensure the safety of both the crew and the spacecraft. NASA’s Johnson Space Center has recently developed a microbial swab kit specifically for use during astronaut Extravehicular Activity (EVA). The EVA swab kit is designed to be held in an astronauts’ bulky gloves and or by a robot’s manipulator, and is thus suitable for microbial sample collection in remote and extreme locations. The ability of crew members to successfully use the EVA swab kit to sample the microbial communities of an Analog habitat was tested, resulting in the successful characterization of the microbial communities within this unique habitat. Results: Several samples (floor, dry wall, glass, and metal surfaces) were collected for estimating cultivable, viable, and metabolically active microbial population using the EVA swab kit. The cultivable microbial population ranged from below the detection limit (BDL) to 106 CFU/sample and their identity was characterized using molecular methods. Next-generation sequencing (NGS; both 16S rRNA amplicon and shotgun) were used to characterize the microbial dynamics, community profiles and functional analysis (metabolic, virulence, and antimicrobial resistance). The 16S rRNA amplicon sequencing revealed abundance of viable Actinobacteria (Brevibacterium, Nesternkonia, Mycobacterium, Pseudonocardia and Corynebacterium), Firmicutes (Virgibacillus, Staphylococcus and Oceanobacillus) and Proteobacteria (esp. Acinetobacter) on floor/wall surfaces, while members of Firmicutes (Leuconostocaceae) and Proteobacteria (Enterobacteriaceae) were high on the glass/metal surfaces. Through non-metric multidimensional scaling (NMDS) determined from both 16S rRNA and metagenomic analyses revealed differential microbial speciation between floor/wall surfaces and glass/metal surfaces. Conclusion: This study provides the first assessment of monitoring cultivable and viable microorganisms from a closed spacecraft Analog submerged habitat surfaces. Several statistical treatments suggested that the largest selective pressure on the microbial community structure was the surface type since different kinds of microorganisms were observed in the floor/dry wall surfaces when compared to the metal/glass surfaces, these samples also consistently grouped separately. The metal/glass surfaces had less complex community, lower bio-burden, and more closely resembled the controls. These results indicated that material choice is crucial when building closed habitats, even if they are simply analogs. Despite our results indicating the strong role that surfaces play in selecting for the live/viable microbial communities, our study also shows that there is a shared background community of non-viable microorganisms throughout the Analog habitat. Finally, the microbial ecology of the submerged Analog habitat differs greatly from that of previously studied Analog habitats, while a few species were associated with previously cultivated isolates from the International Space Station and MIR spacecraft.

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Improved microbial community characterization of 16S rRNA via metagenome hybridization capture enrichment

10.1101/2020.12.18.423101 ◽

2020 ◽

Author(s):

Megan Sarah Beaudry ◽

Jincheng Wang ◽

Troy Kieran ◽

Jesse Thomas ◽

Natalia Juliana Bayona-Vasquez ◽

...

Keyword(s):

16S Rrna ◽

Sequence Similarity ◽

Rrna Gene ◽

Metagenomic Sequencing ◽

Sequencing Data ◽

16S Rrna Sequence ◽

Shotgun Metagenomics ◽

Reference Databases ◽

Rrna Sequences ◽

16S Rrna Sequences

Environmental microbial diversity is often investigated from a molecular perspective using 16S ribosomal RNA (rRNA) gene amplicons and shotgun metagenomics. While amplicon methods are fast, low-cost, and have curated reference databases, they can suffer from amplification bias and are limited in genomic scope. In contrast, shotgun metagenomic methods sample more genomic regions with fewer sequence acquisition biases. However, shotgun metagenomic sequencing is much more expensive (even with moderate sequencing depth) and computationally challenging. Here, we develop a set of 16S rRNA sequence capture baits that offer a potential middle ground with the advantages from both approaches for investigating microbial communities. These baits cover the diversity of all 16S rRNA sequences available in the Greengenes (v. 13.5) database, with no sequence having < 80% sequence similarity to at least one bait for all segments of 16S. The use of our baits provide comparable results to 16S amplicon libraries and shotgun metagenomic libraries when assigning taxonomic units from 16S sequences within the metagenomic reads. We demonstrate that 16S rRNA capture baits can be used on a range of microbial samples (i.e., mock communities and rodent fecal samples) to increase the proportion of 16S rRNA sequences (average >400-fold) and decrease analysis time to obtain consistent community assessments. Furthermore, our study reveals that bioinformatic methods used to analyze sequencing data may have a greater influence on estimates of community composition than library preparation method used, likely in part to the extent and curation of the reference databases considered.

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Genomic variation of microbial populations on a continuous 10,000-year sediment sequence from Lake Cadagno (Piora Valley, Switzerland)

10.5194/egusphere-egu21-8230 ◽

2021 ◽

Author(s):

Paula Catalina Rodriguez Ramirez ◽

Jasmine Berg ◽

Longhui Deng ◽

Hendrik Vogel ◽

Mark A. Lever ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Sulfate Reduction ◽

Microbial Populations ◽

Gene Copy ◽

Sulfur Cycling ◽

Rrna Gene ◽

Sediment Layer ◽

Metagenomic Sequencing ◽

Sulfate Reducing

Lake Cadagno is a meromictic Alpine lake located in the Piora Valley, Switzerland. In 2019, a 10,000-year (10 m)sediment sequence was collected and found to contain three main lithological units: glacial sediment deposited under oxic conditions; a Mn-rich and organic-matter-rich sediment layer deposited during the transition from an oxic late-glacial lake to the onset of anoxia, and dark, sulfidic sediments deposited during the period of euxinia to the present. This study investigates the relationships between the physical-chemical properties and microorganisms of the sediment sequenceusing genome-resolved and targeted metagenomics.&#160; &#160;Results show that 16S rRNA gene abundance peaks in upper 1-32 cm of the sediment core (108 copies per gram of sediment) and decreases with depth. The abundance of a marker gene for sulfate reduction, dsrB, is positively correlated to 16S rRNA gene copy numbers, decreasing with depth from approximately 108 copies per gram of sediment in the top 30 cm to 104 gene copies per gram of sediment at 900 cm below the sediment depth.&#160; These results suggest that sulfate-reducing microbial communities in surface sediments harvest the bioavailable oxidized sulfur inorganic species. In contrast, the presence of sulfate-reducing genes in sediments with sulfate concentrations below detection may indicate the engagement of microbial populations in sulfur cycling using alternative metabolic strategies (e.g. secondary fermentation).&#160;Moreover, a clear differentiation between surface and deep sediment communities is observed. Sequencing of dsrB amplicons show a decrease in dsrB sequence richness with depth and sediment age. A clear transition from a surface section dominated (>80% relative abundance) by Deltaproteobacteria-related dsrB sequences from well-studied groups, to a deeper section below 40 cm dominated by a group of unclassified dsrB sequences most likely related to Firmicutes or Chloroflexi is also observed. The identity of these unclassified dsrB sequences will be determined by genome-resolved metagenomic sequencing (currently in progress). Furthermore, these analyses will give information on the presence of complete sulfate-reduction pathways and/or genes related to sulfur cycling in these microbial groups. By reconstructing the genomes of sulfate reducers and other microbial populations throughout the core, we will investigate whether there are genomic changes associated with the main geochemical trends. This work will enable us to assess the influence of a changing lake with the evolution of sediment-dwelling prokaryotic populations over thousands of years.&#160;&#160;&#160;

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OGUs enable effective, phylogeny-aware analysis of even shallow metagenome community structures

10.1101/2021.04.04.438427 ◽

2021 ◽

Author(s):

Qiyun Zhu ◽

Shi Huang ◽

Antonio Gonzalez ◽

Imran McGrath ◽

Daniel McDonald ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Human Microbiome ◽

Human Microbiome Project ◽

Rrna Gene ◽

Metagenomic Sequencing ◽

Shotgun Metagenomics ◽

Biologically Relevant ◽

Metagenome Analysis ◽

Host Sex

We introduce Operational Genomic Unit (OGU), a metagenome analysis strategy that directly exploits sequence alignment hits to individual reference genomes as the minimum unit for assessing the diversity of microbial communities and their relevance to environmental factors. This approach is independent from taxonomic classification, granting the possibility of maximal resolution of community composition, and organizes features into an accurate hierarchy using a phylogenomic tree. The outputs are suitable for contemporary analytical protocols for community ecology, differential abundance and supervised learning while supporting phylogenetic methods, such as UniFrac and phylofactorization, that are seldomly applied to shotgun metagenomics despite being prevalent in 16S rRNA gene amplicon studies. As demonstrated in one synthetic and two real-world case studies, the OGU method produces biologically meaningful patterns from microbiome datasets. Such patterns further remain detectable at very low metagenomic sequencing depths. Compared with taxonomic unit-based analyses implemented in currently adopted metagenomics tools, and the analysis of 16S rRNA gene amplicon sequence variants, this method shows superiority in informing biologically relevant insights, including stronger correlation with body environment and host sex on the Human Microbiome Project dataset, and more accurate prediction of human age by the gut microbiomes in the Finnish population. We provide Woltka, a bioinformatics tool to implement this method, with full integration with the QIIME 2 package and the Qiita web platform, to facilitate OGU adoption in future metagenomics studies.

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Faculty Opinions recommendation of Low Maternal Microbiota Sharing across Gut, Breast Milk and Vagina, as Revealed by 16S rRNA Gene and Reduced Metagenomic Sequencing.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.733207420.793548246 ◽

2018 ◽

Author(s):

Gregor Reid

Keyword(s):

Breast Milk ◽

16S Rrna ◽

16S Rrna Gene ◽

Rrna Gene ◽

Metagenomic Sequencing

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Comparison between 16S rRNA and shotgun sequencing data for the taxonomic characterization of the gut microbiota

Scientific Reports ◽

10.1038/s41598-021-82726-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Francesco Durazzi ◽

Claudia Sala ◽

Gastone Castellani ◽

Gerardo Manfreda ◽

Daniel Remondini ◽

...

Keyword(s):

16S Rrna ◽

Gut Microbiota ◽

16S Rrna Gene ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Shotgun Sequencing ◽

Rrna Gene ◽

Metagenomic Sequencing ◽

Experimental Conditions ◽

Rrna Gene Sequencing

AbstractIn this paper we compared taxonomic results obtained by metataxonomics (16S rRNA gene sequencing) and metagenomics (whole shotgun metagenomic sequencing) to investigate their reliability for bacteria profiling, studying the chicken gut as a model system. The experimental conditions included two compartments of gastrointestinal tracts and two sampling times. We compared the relative abundance distributions obtained with the two sequencing strategies and then tested their capability to distinguish the experimental conditions. The results showed that 16S rRNA gene sequencing detects only part of the gut microbiota community revealed by shotgun sequencing. Specifically, when a sufficient number of reads is available, Shotgun sequencing has more power to identify less abundant taxa than 16S sequencing. Finally, we showed that the less abundant genera detected only by shotgun sequencing are biologically meaningful, being able to discriminate between the experimental conditions as much as the more abundant genera detected by both sequencing strategies.

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Microdiversity and phylogeographic diversification of bacterioplankton in pelagic freshwater systems revealed through long-read amplicon sequencing

Microbiome ◽

10.1186/s40168-020-00974-y ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Yusuke Okazaki ◽

Shohei Fujinaga ◽

Michaela M. Salcher ◽

Cristiana Callieri ◽

Atsushi Tanaka ◽

...

Keyword(s):

16S Rrna ◽

Regional Scale ◽

Scale Up ◽

Amplicon Sequencing ◽

Freshwater Ecosystems ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

Metagenomic Sequencing ◽

Long Read

Abstract Background Freshwater ecosystems are inhabited by members of cosmopolitan bacterioplankton lineages despite the disconnected nature of these habitats. The lineages are delineated based on > 97% 16S rRNA gene sequence similarity, but their intra-lineage microdiversity and phylogeography, which are key to understanding the eco-evolutional processes behind their ubiquity, remain unresolved. Here, we applied long-read amplicon sequencing targeting nearly full-length 16S rRNA genes and the adjacent ribosomal internal transcribed spacer sequences to reveal the intra-lineage diversities of pelagic bacterioplankton assemblages in 11 deep freshwater lakes in Japan and Europe. Results Our single nucleotide-resolved analysis, which was validated using shotgun metagenomic sequencing, uncovered 7–101 amplicon sequence variants for each of the 11 predominant bacterial lineages and demonstrated sympatric, allopatric, and temporal microdiversities that could not be resolved through conventional approaches. Clusters of samples with similar intra-lineage population compositions were identified, which consistently supported genetic isolation between Japan and Europe. At a regional scale (up to hundreds of kilometers), dispersal between lakes was unlikely to be a limiting factor, and environmental factors or genetic drift were potential determinants of population composition. The extent of microdiversification varied among lineages, suggesting that highly diversified lineages (e.g., Iluma-A2 and acI-A1) achieve their ubiquity by containing a consortium of genotypes specific to each habitat, while less diversified lineages (e.g., CL500-11) may be ubiquitous due to a small number of widespread genotypes. The lowest extent of intra-lineage diversification was observed among the dominant hypolimnion-specific lineage (CL500-11), suggesting that their dispersal among lakes is not limited despite the hypolimnion being a more isolated habitat than the epilimnion. Conclusions Our novel approach complemented the limited resolution of short-read amplicon sequencing and limited sensitivity of the metagenome assembly-based approach, and highlighted the complex ecological processes underlying the ubiquity of freshwater bacterioplankton lineages. To fully exploit the performance of the method, its relatively low read throughput is the major bottleneck to be overcome in the future.

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Metagenome-validated Parallel Amplicon Sequencing and Text Mining-based Annotations for Simultaneous Profiling of Bacteria and Fungi: Vaginal Microbiome and Mycobiota in Healthy Women

10.21203/rs.3.rs-321778/v1 ◽

2021 ◽

Author(s):

Seppo Virtanen ◽

Schahzad Saqib ◽

Tinja Kanerva ◽

Pekka Nieminen ◽

Ilkka Kalliala ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Cost Effective ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Extensive Literature ◽

Metagenomic Sequencing ◽

Text Extraction ◽

Healthy Women ◽

Bacteria And Fungi

Abstract Background: Amplicon sequencing of kingdom-specific tags such as 16S rRNA gene for bacteria and internal transcribed spacer (ITS) region for fungi are widely used for investigating microbial populations. So far most human studies have focused on bacteria while studies on host-associated fungi in health and disease have only recently started to accumulate. To enable cost-effective parallel analysis of bacterial and fungal communities in human and environmental samples, we developed a method where 16S rRNA gene and ITS-1 amplicons were pooled together for a single Illumina MiSeq or HiSeq run and analysed after primer-based segregation. Taxonomic assignments were performed with Blast in combination with an iterative text-extraction based filtration approach, which uses extensive literature records from public databases to select the most probable hits that were further validated by shotgun metagenomic sequencing. Results: Using 50 vaginal samples, we show that the combined run provides comparable results on bacterial composition and diversity to conventional 16S rRNA gene amplicon sequencing. The text-extraction-based taxonomic assignment guided tool provided ecosystem specific annotations that were confirmed by Metagenomic Phylogenetic Analysis (MetaPhlAn). The metagenome analysis revealed distinct functional differences between the bacterial community types while fungi were undetected, despite being identified in all samples based on ITS amplicons. Co-abundance analysis of bacteria and fungi did not show strong between-kingdom correlations within the vaginal ecosystem of healthy women.Conclusion: Combined amplicon sequencing for bacteria and fungi provides a simple and cost-effective method for simultaneous analysis of microbiota and mycobiota within the same samples. Text extraction-based annotation tool facilitates the characterization and interpretation of defined microbial communities from rapidly accumulating sequencing and metadata readily available through public databases.

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Alone Yet Not Alone: Frankia Lives Under the Same Roof With Other Bacteria in Actinorhizal Nodules

Frontiers in Microbiology ◽

10.3389/fmicb.2021.749760 ◽

2021 ◽

Vol 12 ◽

Author(s):

Faten Ghodhbane-Gtari ◽

Timothy D’Angelo ◽

Abdellatif Gueddou ◽

Sabrine Ghazouani ◽

Maher Gtari ◽

...

Keyword(s):

16S Rrna ◽

Plant Growth ◽

16S Rrna Gene ◽

Root Nodules ◽

Actinorhizal Plants ◽

Rrna Gene ◽

Plant Growth Promoting Bacteria ◽

Metagenomic Sequencing ◽

Plant Growth Promoting ◽

Growth Promoting

Actinorhizal plants host mutualistic symbionts of the nitrogen-fixing actinobacterial genus Frankia within nodule structures formed on their roots. Several plant-growth-promoting bacteria have also been isolated from actinorhizal root nodules, but little is known about them. We were interested investigating the in planta microbial community composition of actinorhizal root nodules using culture-independent techniques. To address this knowledge gap, 16S rRNA gene amplicon and shotgun metagenomic sequencing was performed on DNA from the nodules of Casuarina glauca. DNA was extracted from C. glauca nodules collected in three different sampling sites in Tunisia, along a gradient of aridity ranging from humid to arid. Sequencing libraries were prepared using Illumina NextEra technology and the Illumina HiSeq 2500 platform. Genome bins extracted from the metagenome were taxonomically and functionally profiled. Community structure based off preliminary 16S rRNA gene amplicon data was analyzed via the QIIME pipeline. Reconstructed genomes were comprised of members of Frankia, Micromonospora, Bacillus, Paenibacillus, Phyllobacterium, and Afipia. Frankia dominated the nodule community at the humid sampling site, while the absolute and relative prevalence of Frankia decreased at the semi-arid and arid sampling locations. Actinorhizal plants harbor similar non-Frankia plant-growth-promoting-bacteria as legumes and other plants. The data suggests that the prevalence of Frankia in the nodule community is influenced by environmental factors, with being less abundant under more arid environments.

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