Growth and Population Dynamics of the Anaerobic Fe(II)-Oxidizing and Nitrate-Reducing Enrichment Culture KS

ABSTRACTMost isolated nitrate-reducing Fe(II)-oxidizing microorganisms are mixotrophic, meaning that Fe(II) is chemically oxidized by nitrite that forms during heterotrophic denitrification, and it is debated to which extent Fe(II) is enzymatically oxidized. One exception is the chemolithoautotrophic enrichment culture KS, a consortium consisting of a dominant Fe(II) oxidizer,Gallionellaceaesp., and less abundant heterotrophic strains (e.g.,Bradyrhizobiumsp.,Nocardioidessp.). Currently, this is the only nitrate-reducing Fe(II)-oxidizing culture for which autotrophic growth has been demonstrated convincingly for many transfers over more than 2 decades. We used 16S rRNA gene amplicon sequencing and physiological growth experiments to analyze the community composition and dynamics of culture KS with various electron donors and acceptors. Under autotrophic conditions, an operational taxonomic unit (OTU) related to known microaerophilic Fe(II) oxidizers within the familyGallionellaceaedominated culture KS. With acetate as an electron donor, most 16S rRNA gene sequences were affiliated withBradyrhizobiumsp.Gallionellaceaesp. not only was able to oxidize Fe(II) under autotrophic and mixotrophic conditions but also survived over several transfers of the culture on only acetate, although it then lost the ability to oxidize Fe(II).Bradyrhizobiumspp. became and remained dominant when culture KS was cultivated for only one transfer under heterotrophic conditions, even when conditions were reverted back to autotrophic in the next transfer. This study showed a dynamic microbial community in culture KS that responded to changing substrate conditions, opening up questions regarding carbon cross-feeding, metabolic flexibility of the individual strains in KS, and the mechanism of Fe(II) oxidation by a microaerophile in the absence of O2.IMPORTANCENitrate-reducing Fe(II)-oxidizing microorganisms are present in aquifers, soils, and marine and freshwater sediments. Most nitrate-reducing Fe(II) oxidizers known are mixotrophic, meaning that they need organic carbon to continuously oxidize Fe(II) and grow. In these microbes, Fe(II) was suggested to be chemically oxidized by nitrite that forms during heterotrophic denitrification, and it remains unclear whether or to what extent Fe(II) is enzymatically oxidized. In contrast, the enrichment culture KS was shown to oxidize Fe(II) autotrophically coupled to nitrate reduction. This culture contains the designated Fe(II) oxidizerGallionellaceaesp. and several heterotrophic strains (e.g.,Bradyrhizobiumsp.). We showed that culture KS is able to metabolize Fe(II) and a variety of organic substrates and is able to adapt to dynamic environmental conditions. When the community composition changed andBradyrhizobiumbecame the dominant community member, Fe(II) was still oxidized byGallionellaceaesp., even when culture KS was cultivated with acetate/nitrate [Fe(II) free] before being switched back to Fe(II)/nitrate.

Download Full-text

16S rRNA Gene Amplicon Sequencing Data of Tailing and Nontailing Rhizosphere Soils of Mimosa pudica from a Heavy Metal-Contaminated Ex-Tin Mining Area

Microbiology Resource Announcements ◽

10.1128/mra.00761-20 ◽

2020 ◽

Vol 9 (42) ◽

Author(s):

Saidu Abdullahi ◽

Hazzeman Haris ◽

Kamarul Z. Zarkasi ◽

Hamzah G. Amir

Keyword(s):

Heavy Metal ◽

16S Rrna ◽

16S Rrna Gene ◽

Sequence Data ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Mimosa Pudica ◽

Sequencing Data ◽

Content Type ◽

Rhizosphere Soils

ABSTRACT The 16S rRNA gene amplicon sequence data from tailing and nontailing rhizosphere soils of Mimosa pudica from a heavy metal-contaminated area are reported here. Diverse bacterial taxa were represented in the results, and the most dominant phyla were Proteobacteria (41.2%), Acidobacteria (17.1%), and Actinobacteria (14.4%).

Download Full-text

16S rRNA Gene Amplicon Sequencing of Gut Microbiota from Naked Carp (Gymnocypris przewalskii) in Qinghai Lake, China

Microbiology Resource Announcements ◽

10.1128/mra.00374-21 ◽

2021 ◽

Vol 10 (23) ◽

Author(s):

Fayan Wang ◽

Yu Liu ◽

Guangxin Li ◽

Xi Yang ◽

Qiang Gao

Keyword(s):

16S Rrna ◽

Gut Microbiota ◽

16S Rrna Gene ◽

Amplicon Sequencing ◽

Qinghai Lake ◽

Second Grade ◽

Rrna Gene ◽

Content Type ◽

Gymnocypris Przewalskii ◽

State Protection

Naked carp ( Gymnocypris przewalskii ) is a second-grade animal under state protection of China. We report 16S rRNA gene amplicon analysis of the gut microbiota of Gymnocypris przewalskii . The three most abundant phyla are Tenericutes , Proteobacteria , and Fusobacteria , and the six most abundant genera are Aeromonas , Clostridium , Cetobacterium , Shewanella , Prochlorococcus , and Vibrio .

Download Full-text

Environmental Factors Affect Acidobacterial Communities below the Subgroup Level in Grassland and Forest Soils

Applied and Environmental Microbiology ◽

10.1128/aem.01325-12 ◽

2012 ◽

Vol 78 (20) ◽

pp. 7398-7406 ◽

Cited By ~ 170

Author(s):

Astrid Naether ◽

Bärbel U. Foesel ◽

Verena Naegele ◽

Pia K. Wüst ◽

Jan Weinert ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Community Composition ◽

Plant Diversity ◽

Forest Soils ◽

Denaturing Gradient Gel Electrophoresis ◽

Vascular Plant ◽

Environmental Parameters ◽

Rrna Gene ◽

Content Type

ABSTRACTIn soil,Acidobacteriaconstitute on average 20% of all bacteria, are highly diverse, and are physiologically activein situ. However, their individual functions and interactions with higher taxa in soil are still unknown. Here, potential effects of land use, soil properties, plant diversity, and soil nanofauna on acidobacterial community composition were studied by cultivation-independent methods in grassland and forest soils from three different regions in Germany. The analysis of 16S rRNA gene clone libraries representing all studied soils revealed that grassland soils were dominated by subgroup Gp6 and forest soils by subgroup Gp1Acidobacteria. The analysis of a large number of sites (n= 57) by 16S rRNA gene fingerprinting methods (terminal restriction fragment length polymorphism [T-RFLP] and denaturing gradient gel electrophoresis [DGGE]) showed thatAcidobacteriadiversities differed between grassland and forest soils but also among the three different regions. Edaphic properties, such as pH, organic carbon, total nitrogen, C/N ratio, phosphorus, nitrate, ammonium, soil moisture, soil temperature, and soil respiration, had an impact on community composition as assessed by fingerprinting. However, interrelations with environmental parameters among subgroup terminal restriction fragments (T-RFs) differed significantly, e.g., different Gp1 T-RFs correlated positively or negatively with nitrogen content. Novel significant correlations ofAcidobacteriasubpopulations (i.e., individual populations within subgroups) with soil nanofauna and vascular plant diversity were revealed only by analysis of clone sequences. Thus, for detecting novel interrelations of environmental parameters withAcidobacteria, individual populations within subgroups have to be considered.

Download Full-text

Thiophaeococcus fuscus sp. nov., isolated from a lagoon

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.062182-0 ◽

2014 ◽

Vol 64 (Pt_8) ◽

pp. 2528-2533 ◽

Cited By ~ 6

Author(s):

B. Divyasree ◽

K. V. N. S. Lakshmi ◽

Ch. Sasikala ◽

Ch. V. Ramana

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Type Strain ◽

Type Species ◽

Enrichment Culture ◽

Sequence Similarity ◽

Molecular Evidence ◽

Rrna Gene ◽

Content Type ◽

Link Type

A brown-coloured bacterium, designated strain JA633T, was purified from a photoheterotrophic enrichment culture obtained from black sand of a lagoon. Cells of strain JA633T were coccoid–spherical, Gram-stain-negative and motile by means of polar flagella. Strain JA633T had an obligate requirement for NaCl and could tolerate up to 4 % (w/v) NaCl. Internal photosynthetic membranes were present as vesicles. Photo-organoheterotrophy was the only growth mode observed. Strain JA633T contained bacteriochlorophyll a and a major (>85 %) unidentified carotenoid of the spirilloxanthin series. Thiamine and p-aminobenzoic acid were required for growth. Major fatty acids were C18 : 1ω7c/C18 : 1ω6c, C16 : 0 and C16 : 1ω7c/C16 : 1ω6c. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphotidylcholine and an unknown aminophospholipid were the major polar lipids in strain JA633T. The DNA G+C content of strain JA633T was 64.5 mol%. Strain JA633T shared highest 16S rRNA gene sequence similarity with the type strains of Thiorhodococcus kakinadensis (96.9 %), Thiophaeococcus mangrovi (96.3 %) and Thiorhodococcus bheemlicus (96.2 %), which belonged to the class Gammaproteobacteria . However, phylogenetic analysis based on 16S rRNA gene sequences showed that strain JA633T formed a separate clade along with Thiophaeococcus mangrovi JA304T whereas the members of the genus Thiorhodococcus remained as two distinct phylogenetic lineages. Based on morphological, physiological, chemotaxonomic and molecular evidence, strain JA633T was significantly different from the type strain of Thiophaeococcus mangrovi of the family Chromatiaceae . It is thus proposed that the strain be classified as a representative of a novel species, for which the name Thiophaeococcus fuscus sp. nov. is proposed. The type strain is JA633T ( = KCTC 15337T = NBRC 109958T).

Download Full-text

High-Resolution Melt Analysis for Rapid Comparison of Bacterial Community Compositions

Applied and Environmental Microbiology ◽

10.1128/aem.03923-13 ◽

2014 ◽

Vol 80 (12) ◽

pp. 3568-3575 ◽

Cited By ~ 29

Author(s):

Mathis Hjort Hjelmsø ◽

Lars Hestbjerg Hansen ◽

Jacob Bælum ◽

Louise Feld ◽

William E. Holben ◽

...

Keyword(s):

High Resolution ◽

Bacterial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Community Composition ◽

Bacterial Community Composition ◽

Amplicon Sequencing ◽

Rrna Gene ◽

High Resolution Melt ◽

Hrm Analysis

ABSTRACTIn the study of bacterial community composition, 16S rRNA gene amplicon sequencing is today among the preferred methods of analysis. The cost of nucleotide sequence analysis, including requisite computational and bioinformatic steps, however, takes up a large part of many research budgets. High-resolution melt (HRM) analysis is the study of the melt behavior of specific PCR products. Here we describe a novel high-throughput approach in which we used HRM analysis targeting the 16S rRNA gene to rapidly screen multiple complex samples for differences in bacterial community composition. We hypothesized that HRM analysis of amplified 16S rRNA genes from a soil ecosystem could be used as a screening tool to identify changes in bacterial community structure. This hypothesis was tested using a soil microcosm setup exposed to a total of six treatments representing different combinations of pesticide and fertilization treatments. The HRM analysis identified a shift in the bacterial community composition in two of the treatments, both including the soil fumigant Basamid GR. These results were confirmed with both denaturing gradient gel electrophoresis (DGGE) analysis and 454-based 16S rRNA gene amplicon sequencing. HRM analysis was shown to be a fast, high-throughput technique that can serve as an effective alternative to gel-based screening methods to monitor microbial community composition.

Download Full-text

Pelobacter seleniigenes sp. nov., a selenate-respiring bacterium

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.64980-0 ◽

2007 ◽

Vol 57 (9) ◽

pp. 1937-1942 ◽

Cited By ~ 28

Author(s):

Priya Narasingarao ◽

Max M. Häggblom

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Enrichment Culture ◽

Sequence Similarity ◽

Carbon Substrate ◽

Elemental Selenium ◽

Rrna Gene ◽

Organic Substrates ◽

Phylogenetic Grouping ◽

Metabolic Properties

Strain KMT is a novel bacterium with the unique metabolic abilities of being able to respire selenate as the electron acceptor using acetate as the carbon substrate and possessing the ability to grow fermentatively on short-chain organic acids such as lactate, citrate and pyruvate. Strain KMT was isolated from a sediment enrichment culture of a highly impacted wetland system in New Jersey, USA. Strain KMT is able to reduce selenate as well as selenite to elemental selenium. The unique metabolic capabilities of strain KMT include the respiration of nitrate, poorly crystalline Fe(III) and anthraquinone disulfonate. Phylogenetic analysis of the 16S rRNA gene of the novel isolate indicates that strain KMT groups within the family Geobacteraceae in the class Deltaproteobacteria with approximately 96–97 % 16S rRNA gene sequence similarity to the closest known organisms Malonomonas rubra Gra Mal 1T, Pelobacter acidigallici Ma Gal 2T and species of the genus Desulfuromusa. Recognized species of the genera Malonomonas and Pelobacter cannot use any inorganic electron acceptors, while strains of the genus Desulfuromusa do not ferment organic substrates. This contrasts with the ability of strain KMT to ferment organic compounds as well as to couple selenate reduction to acetate utilization. Based on 16S rRNA gene phylogeny and metabolic properties, strain KMT represents a novel species for which the name Pelobacter seleniigenes sp. nov. (type strain KMT=DSM 18267T=ATCC BAA-1388T) is proposed. Based on the phylogenetic grouping of species of the genus Pelobacter within the Desulfuromusa cluster, it is suggested that Malonomonas rubra Gra Mal 1T should also be included in this group.

Download Full-text

Bacterial Diversity Profiling of the New Zealand Parasitic Blowfly Lucilia sericata Based on 16S rRNA Gene Amplicon Sequencing

Microbiology Resource Announcements ◽

10.1128/mra.00257-21 ◽

2021 ◽

Vol 10 (19) ◽

Author(s):

Nikola Palevich ◽

Paul H. Maclean ◽

Luis Carvalho ◽

Ruy Jauregui

Keyword(s):

New Zealand ◽

16S Rrna ◽

16S Rrna Gene ◽

Bacterial Diversity ◽

Sequence Data ◽

Amplicon Sequencing ◽

Lucilia Sericata ◽

Rrna Gene ◽

Data Set ◽

Content Type

ABSTRACT Here, we present a 16S rRNA gene amplicon sequence data set and profiles demonstrating the bacterial diversity of larval and adult Lucilia sericata, collected from Ashhurst, New Zealand (May 2020). The two dominant genera among adult male and female L. sericata were Serratia and Morganella (phylum Proteobacteria), while the larvae were also dominated by the genera Lactobacillus, Carnobacterium, and Lactococcus (phylum Firmicutes).

Download Full-text

Deciphering the Root Endosphere Microbiome of the Desert Plant Alhagi sparsifolia for Drought Resistance-Promoting Bacteria

Applied and Environmental Microbiology ◽

10.1128/aem.02863-19 ◽

2020 ◽

Vol 86 (11) ◽

Author(s):

Lei Zhang ◽

Weipeng Zhang ◽

Qiqi Li ◽

Rui Cui ◽

Zhuo Wang ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Drought Resistance ◽

Amplicon Sequencing ◽

Disease Suppression ◽

Rrna Gene ◽

Desert Plant ◽

Desert Plants ◽

Alhagi Sparsifolia ◽

Content Type

ABSTRACT Drought is among the most destructive abiotic stresses limiting crop growth and yield worldwide. Although most research has focused on the contribution of plant-associated microbial communities to plant growth and disease suppression, far less is known about the microbes involved in drought resistance among desert plants. In the present study, we applied 16S rRNA gene amplicon sequencing to determine the structure of rhizosphere and root endosphere microbiomes of Alhagi sparsifolia. Compared to those of the rhizosphere, endosphere microbiomes had lower diversity but contained several taxa with higher relative abundance; many of these taxa were also present in the roots of other desert plants. We isolated a Pseudomonas strain (LTGT-11-2Z) that was prevalent in root endosphere microbiomes of A. sparsifolia and promoted drought resistance during incubation with wheat. Complete genome sequencing of LTGT-11-2Z revealed 1-aminocyclopropane-1-carboxylate deaminases, siderophore, spermidine, and colanic acid biosynthetic genes, as well as type VI secretion system (T6SS) genes, which are likely involved in biofilm formation and plant-microbe interactions. Together, these results indicate that drought-enduring plants harbor bacterial endophytes favorable to plant drought resistance, and they suggest that novel endophytic bacterial taxa and gene resources may be discovered among these desert plants. IMPORTANCE Understanding microbe-mediated plant resistance to drought is important for sustainable agriculture. We performed 16S rRNA gene amplicon sequencing and culture-dependent functional analyses of Alhagi sparsifolia rhizosphere and root endosphere microbiomes and identified key endophytic bacterial taxa and their genes facilitating drought resistance in wheat. This study improves our understanding of plant drought resistance and provides new avenues for drought resistance improvement in crop plants under field conditions.

Download Full-text

Caproicibacter fermentans gen. nov., sp. nov., a new caproate-producing bacterium and emended description of the genus Caproiciproducens

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.004283 ◽

2020 ◽

Vol 70 (7) ◽

pp. 4269-4279 ◽

Cited By ~ 12

Author(s):

Maximilian Flaiz ◽

Tina Baur ◽

Sven Brahner ◽

Anja Poehlein ◽

Rolf Daniel ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Type Species ◽

Enrichment Culture ◽

Bacterial Species ◽

Rrna Gene ◽

Strictly Anaerobic ◽

Content Type ◽

Link Type ◽

The Family

A strictly anaerobic bacterial strain designated EA1T was isolated from an enrichment culture inoculated with biogas reactor content. Cells of strain EA1T are spore-forming rods (1–3×0.4–0.8 µm) and stain Gram-negative, albeit they possess a Gram-positive type of cell-wall ultrastructure. Growth of strain EA1T was observed at 30 and 37 °C and within a pH range of pH 5–9. The major components recovered in the fatty acid fraction were C14:0, C16:0, C16:0 DMA (dimethyl acetal) and C16:1 ω7c. Strain EA1T fermented several mono- and disaccharides. Metabolic end products from fructose were acetate, butyrate, caproate and lactate. Furthermore, ethanol, CO2 and H2 were identified as products. The genome consists of a chromosome (3.9 Mbp) with 3797 predicted protein-encoding genes and a G+C content of 51.25 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain EA1T represents a novel taxon within the family Oscillospiraceae . The most closely related type strains of EA1T, based on 16S rRNA gene sequence identity, are Caproiciproducens galactitolivorans BS-1T (94.9 %), [ Clostridium ] leptum DSM 753T (93.8 %), [ Clostridium ] sporosphaeroides DSM 1294T (91.7 %) and Ruminococcus bromii ATCC 27255T (91.0 %). Further phenotypic characteristics of strain EA1T differentiate it from related, validly described bacterial species. Strain EA1T represents a novel genus and novel species within the family Oscillospiraceae . The proposed name is Caproicibacter fermentans gen. nov., sp. nov. The type strain is EA1T (DSM 107079T=JCM 33110T).

Download Full-text

Response to Edaphoclimatic Conditions and Crop Management of the Bacterial Microbiome of Musa acuminata Rhizosphere Profiled by 16S rRNA Gene Amplicon Sequencing

Microbiology Resource Announcements ◽

10.1128/mra.01437-20 ◽

2021 ◽

Vol 10 (10) ◽

Author(s):

Francisco J. De la Torre-González ◽

Elisa Fernández-Castillo ◽

Dailen Azaharez-Llorente ◽

Jorge Lara ◽

Enrique Avendaño ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Management Practices ◽

Crop Management ◽

Amplicon Sequencing ◽

Musa Acuminata ◽

Rrna Gene ◽

Content Type ◽

Microbiome Composition ◽

Bacterial Microbiome

ABSTRACT Bacterial rhizospheric microbiomes of Musa acuminata cultivated in farms close to the west and east Mexican coasts and with different climate, soils, and crop management practices were characterized by 16S rRNA gene amplicon sequencing. Results showed that rhizospheric microbiome composition changed along with seasonal weather but were mostly indifferent to soil type.

Download Full-text