DOCSLIB.ORG

Living to the High Extreme: Unraveling the Composition, Structure

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

bioRxiv preprint doi: https://doi.org/10.1101/2021.04.13.439755; this version posted April 16, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. 1 Living to the high extreme: unraveling the composition, structure, 2 and functional insights of bacterial communities thriving in the 3 arsenic-rich Salar de Huasco – Altiplanic ecosystem. 4 5 6 Castro-Severyn, J1,±; Pardo-Esté, C1,2,±; Mendez, KN3; Fortt, J1; Marquez, S3; Molina, F4; 7 Castro-Nallar, E3; Remonsellez, F1,5 * and Saavedra, CP2 *. 8 9 1 Laboratorio de Microbiología Aplicada y Extremófilos, Facultad de Ingeniería y Ciencias 10 Geológicas, Universidad Católica del Norte, Antofagasta, Chile. 11 2 Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad 12 Andres Bello, Santiago, Chile. 13 3 Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, 14 Universidad Andres Bello, Santiago, Chile. 15 4 Sys2Diag, UMR9005 CNRS ALCEDIAG, Montpellier, France 16 5 Centro de Investigación Tecnológica del Agua en el Desierto-CEITSAZA, Universidad 17 Católica del Norte, Antofagasta, Chile. 18 19 ± Juan Castro-Severyn and Coral Pardo-Esté have contributed equally to this work. Author 20 order was determined both by contribution and in order of increasing seniority. 21 22 *Correspondence: Francisco Remonsellez, [email protected] and Claudia P. Saavedra, 23 [email protected]. 24 25 26 Running title: Altiplanic communities living under arsenic stress. 27 28 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.04.13.439755; this version posted April 16, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. 29 ABSTRACT 30 Microbial communities inhabiting extreme environments like Salar de Huasco (SH) are 31 adapted to thrive while exposed to several abiotic pressures and the presence of toxic 32 elements like arsenic (As). Hence, we aimed to uncover the role of arsenic in shaping 33 bacterial composition, structure, and functional potential in five different sites in this 34 Altiplanic wetland using a shotgun metagenomic approach. The sites exhibit wide gradients 35 of arsenic (9 to 321 mg/kg), and our results showed highly diverse communities and a clear 36 dominance exerted by the Proteobacteria and Bacteroidetes phyla. Functional potential 37 analyses showed broadly convergent patterns, contrasting with their great taxonomic 38 variability. Arsenic-related metabolism is different among the five communities, as well as 39 other functional categories like those related to the CH4 and S cycles. Particularly, we found 40 that the distribution and abundance of As-related genes increase, following along the As 41 concentration gradient. Approximately 75% of the detected genes for As-metabolism 42 belong to expulsion mechanisms, being arsJ and arsP pumps related to sites with higher As 43 concentrations and present almost exclusively in Proteobacteria. Furthermore, taxonomic 44 diversity and functional potential are reflected in the 12 reconstructed high-quality MAGs 45 (Metagenome Assembled Genomes) belonging to the Bacteroidetes (5), Proteobacteria (5), 46 Cyanobacteria (1) and Gemmatimonadota (1) phyla. We conclude that SH microbial 47 communities are diverse and possess a broad genetic repertoire to thrive under extreme 48 conditions, including increasing concentrations of the highly toxic As. Finally, this 49 environment represents a reservoir of unknown and undescribed microorganisms, with a 50 great metabolic versatility, which needs further study. 51 52 KEY WORDS: Extremophiles, Metagenomics, Arsenic, MAGs, Altiplano. 53 54 55 IMPORTANCE 56 Microbial communities inhabiting extreme environments are fundamental for maintaining 57 the ecosystems; however, little is known about their potential functions and interactions 2 bioRxiv preprint doi: https://doi.org/10.1101/2021.04.13.439755; this version posted April 16, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. 58 among them. We sampled the microbial communities in Salar de Huasco (SH) in the Chilean 59 Altiplano, a fragile and complex environment that comprises several stresses. We found 60 that microbes in SH are taxonomically diverse; nonetheless, their functional potential seems 61 to have an important convergence degree, suggesting high adaptation levels. Particularly, 62 arsenic metabolism showed differences associated with increasing concentrations of the 63 metalloid throughout the area, and it is effectively exerting a clear and significant pressure 64 over these organisms. Thus, this research´s significance is that we described highly 65 specialized communities thriving in little-explored environments under several pressures, 66 considered analogous of early Earth and other planets, and can have the potential for 67 unraveling technologies to face climate change repercussions in many areas of interest. 68 69 70 INTRODUCTION 71 Extreme environments like high-altitude wetlands select for adaptations in bacterial 72 communities that enable them to thrive. This particular and fragile environment resemble 73 life before the oxygenation of Earth and could serve as models for studying life in other 74 planets. Moreover, microbial communities are critical for maintaining biogeochemical 75 cycles, particularly in extreme environments where there is little presence of other life 76 forms. Therefore, microorganisms are crucial for ecosystems’ health and functioning (1). 77 Salar de Huasco (SH), a high-altitude wetland located in the Chilean Altiplano (20°18’18’’S; 78 68°50’22’’W, Chile) at 3,800 m.a.s.l. is a Ramsar protected site, considered a hotspot for 79 microbial life (2,3). This area is labeled as extreme due to very particular confluence of 80 physicochemical and environmental conditions, like negative water balance, high daily 81 temperature variation, very arid conditions, high salinity, low atmospheric pressure, high 82 solar radiation, presence of arsenic, among other stressors (4, 5, 6, 7, 8, 9). 83 84 In high altitude wetlands, arsenic concentration, moisture availability, and salt 85 concentrations model communities at a small scale (10, 11, 12, 13). The presence of toxic 86 metal(oids), such as arsenic, is one of the main drivers of microbial communities’ 3 bioRxiv preprint doi: https://doi.org/10.1101/2021.04.13.439755; this version posted April 16, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. 87 composition (14), as an important selection pressure originated from natural geochemical 88 processes or human activities. Also, previous studies have determined that the presence of 89 metal(oids) can influence biogeochemical cycles, namely C, N and S, by promoting specific 90 chemical reactions and the enrichment of chemoautotrophs, for example As(III)-oxidizing 91 bacteria that can couple this process with nitrate reduction (15, 16, 17); thus, making 92 relevant to assess the metabolic potential of indigenous microbes and communities. In the 93 North of Chile, the relationship between volcanism activities and the presence of arsenic is 94 a known feature, this geological process has been attributed to hydrothermal conditions 95 such as geysers and fumaroles in the pre-range and high plateau (5). Besides, bacteria that 96 thrive in these environments exhibit arsenic-related genes, including genes associated with 97 methylation (ArsM), oxidation (AioAB, ArxAB), and dissimilatory reduction (ArrAB) (18). The 98 most common resistance mechanism is based on As(III) extrusion from the cell by efflux 99 pumps, which is commonly coupled with As(V) reduction (19). Thus, making the genes from 100 the ars operon the most abundant arsenic resistance markers; the basic requirements 101 comprises the arsenite efflux (ArsB, Acr3) and arsenate reductase (ArsC) (20). 102 103 Arsenic is a crucial element for the microbial community composition and 104 metagenomic approaches have helped to shed some light on this subject. For instance, in 105 Socompa’s stromatolites arsenic resistance is achieved mainly through reduction and 106 expulsion of As(V) via Acr3 efflux pumps reductases (21, 22). Additionally, others have found 107 that the presence of arsenic influenced the microbial communities, and the Rhodococcus 108 genus was significantly enriched in elevated levels of the metalloid in groundwater (14). 109 Furthermore, arsenic mobilization is distributed across a broad phylogenetic lineage in 110 similar ecosystems, as arrA was detected in Betaproteobacteria, Deltaproteobacteria, and 111 Nitrospirae MAGs (23). Also, although arsenic-related genes are widespread, they are not 112 universal, in particular As metabolism genes such as aioA, arrA, arsM, arxA are less common 113 in the environment compared with acr3, arsB, arsC and arsD (24). 114 4 bioRxiv preprint doi: https://doi.org/10.1101/2021.04.13.439755; this version
Recommended publications
  • Low Light Availability Alters Root Exudation and Reduces Putative Beneficial Microorganisms in Seagrass Roots

    Low Light Availability Alters Root Exudation and Reduces Putative Beneficial Microorganisms in Seagrass Roots

    Research Collection Journal Article Low Light Availability Alters Root Exudation and Reduces Putative Beneficial Microorganisms in Seagrass Roots Author(s): Martin, Belinda C.; Gleeson, Deirdre; Statton, John; Siebers, Andre R.; Grierson, Pauline; Ryan, Megan H.; Kendrick, Gary A. Publication Date: 2018-01 Permanent Link: https://doi.org/10.3929/ethz-b-000316064 Originally published in: Frontiers in Microbiology 8, http://doi.org/10.3389/fmicb.2017.02667 Rights / License: Creative Commons Attribution 4.0 International This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library fmicb-08-02667 January 9, 2018 Time: 17:50 # 1 ORIGINAL RESEARCH published: 11 January 2018 doi: 10.3389/fmicb.2017.02667 Low Light Availability Alters Root Exudation and Reduces Putative Beneficial Microorganisms in Seagrass Roots Belinda C. Martin1,2*, Deirdre Gleeson3, John Statton1,2,4, Andre R. Siebers1†, Pauline Grierson1,5, Megan H. Ryan3 and Gary A. Kendrick1,2,4 1 School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia, 2 UWA Oceans Institute, The University of Western Australia, Crawley, WA, Australia, 3 School of Agriculture and Environment, The University of Western Australia, Crawley, WA, Australia, 4 Western Australian Marine Science Institution, Perth, WA, Australia, 5 West Australian Biogeochemistry Centre, School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia Edited by: Seagrass roots host a diverse microbiome that is critical for plant growth and health. Essaid Ait Barka, Composition of microbial communities can be regulated in part by root exudates, but University of Reims Champagne-Ardenne, France the specifics of these interactions in seagrass rhizospheres are still largely unknown.
  • The Subway Microbiome: Seasonal Dynamics and Direct Comparison Of

    The Subway Microbiome: Seasonal Dynamics and Direct Comparison Of

    Gohli et al. Microbiome (2019) 7:160 https://doi.org/10.1186/s40168-019-0772-9 RESEARCH Open Access The subway microbiome: seasonal dynamics and direct comparison of air and surface bacterial communities Jostein Gohli1* , Kari Oline Bøifot1,2, Line Victoria Moen1, Paulina Pastuszek3, Gunnar Skogan1, Klas I. Udekwu4 and Marius Dybwad1,2 Abstract Background: Mass transit environments, such as subways, are uniquely important for transmission of microbes among humans and built environments, and for their ability to spread pathogens and impact large numbers of people. In order to gain a deeper understanding of microbiome dynamics in subways, we must identify variables that affect microbial composition and those microorganisms that are unique to specific habitats. Methods: We performed high-throughput 16S rRNA gene sequencing of air and surface samples from 16 subway stations in Oslo, Norway, across all four seasons. Distinguishing features across seasons and between air and surface were identified using random forest classification analyses, followed by in-depth diversity analyses. Results: There were significant differences between the air and surface bacterial communities, and across seasons. Highly abundant groups were generally ubiquitous; however, a large number of taxa with low prevalence and abundance were exclusively present in only one sample matrix or one season. Among the highly abundant families and genera, we found that some were uniquely so in air samples. In surface samples, all highly abundant groups were also well represented in air samples. This is congruent with a pattern observed for the entire dataset, namely that air samples had significantly higher within-sample diversity. We also observed a seasonal pattern: diversity was higher during spring and summer.
  • Motiliproteus Sediminis Gen. Nov., Sp. Nov., Isolated from Coastal Sediment

    Motiliproteus Sediminis Gen. Nov., Sp. Nov., Isolated from Coastal Sediment

    Antonie van Leeuwenhoek (2014) 106:615–621 DOI 10.1007/s10482-014-0232-2 ORIGINAL PAPER Motiliproteus sediminis gen. nov., sp. nov., isolated from coastal sediment Zong-Jie Wang • Zhi-Hong Xie • Chao Wang • Zong-Jun Du • Guan-Jun Chen Received: 3 April 2014 / Accepted: 4 July 2014 / Published online: 20 July 2014 Ó Springer International Publishing Switzerland 2014 Abstract A novel Gram-stain-negative, rod-to- demonstrated that the novel isolate was 93.3 % similar spiral-shaped, oxidase- and catalase- positive and to the type strain of Neptunomonas antarctica, 93.2 % facultatively aerobic bacterium, designated HS6T, was to Neptunomonas japonicum and 93.1 % to Marino- isolated from marine sediment of Yellow Sea, China. bacterium rhizophilum, the closest cultivated rela- It can reduce nitrate to nitrite and grow well in marine tives. The polar lipid profile of the novel strain broth 2216 (MB, Hope Biol-Technology Co., Ltd) consisted of phosphatidylethanolamine, phosphatidyl- with an optimal temperature for growth of 30–33 °C glycerol and some other unknown lipids. Major (range 12–45 °C) and in the presence of 2–3 % (w/v) cellular fatty acids were summed feature 3 (C16:1 NaCl (range 0.5–7 %, w/v). The pH range for growth x7c/iso-C15:0 2-OH), C18:1 x7c and C16:0 and the main was pH 6.2–9.0, with an optimum at 6.5–7.0. Phylo- respiratory quinone was Q-8. The DNA G?C content genetic analysis based on 16S rRNA gene sequences of strain HS6T was 61.2 mol %. Based on the phylogenetic, physiological and biochemical charac- teristics, strain HS6T represents a novel genus and The GenBank accession number for the 16S rRNA gene T species and the name Motiliproteus sediminis gen.
  • Universidade Federal Do Pampa Campus São Gabriel Programa De Pós-Graduação Stricto Sensu Em Ciências Biológicas

    Universidade Federal Do Pampa Campus São Gabriel Programa De Pós-Graduação Stricto Sensu Em Ciências Biológicas

    UNIVERSIDADE FEDERAL DO PAMPA CAMPUS SÃO GABRIEL PROGRAMA DE PÓS-GRADUAÇÃO STRICTO SENSU EM CIÊNCIAS BIOLÓGICAS PABULO HENRIQUE RAMPELOTTO SEQUENCIAMENTO POR ION TORRENT REVELA PADRÕES DE INTERAÇÃO E DISTRIBUIÇÃO DE COMUNIDADES MICROBIANAS EM UM PERFIL DE SOLO ORNITOGÊNICO DA ILHA SEYMOUR, PENÍNSULA ANTÁRTICA SÃO GABRIEL, RS, BRASIL. 2014 PABULO HENRIQUE RAMPELOTTO SEQUENCIAMENTO POR ION TORRENT REVELA PADRÕES DE INTERAÇÃO E DISTRIBUIÇÃO DE COMUNIDADES MICROBIANAS EM UM PERFIL DE SOLO ORNITOGÊNICO DA ILHA SEYMOUR, PENÍNSULA ANTÁRTICA Dissertação apresentada ao programa de Pós- Graduação Stricto Sensu em Ciências Biológicas da Universidade Federal do Pampa, como requisito parcial para obtenção do Título de Mestre em Ciências Biológicas. Orientador: Prof. Dr. Luiz Fernando Wurdig Roesch São Gabriel 2014 AGRADECIMENTOS À Universidade Federal do Pampa e ao Programa de Pós-Graduação em Ciências Biológicas, por minha formação profissional. Ao Prof. Luiz Fernando Wurdig Roesch, pela orientação durante estes dois anos de mestrado. Ao Prof. Antônio Batista Pereira pela coleta do material durante a XXX Operação Antártica Brasileira (OPERANTAR). À FAPERGS/CAPES, pela concessão da bolsa. RESUMO Neste estudo, foram analisadas e comparadas comunidades bacterianas do solo de uma pinguineira da Ilha Seymour (Península Antártica) em termos de abundância, estrutura, diversidade e rede de interações, a fim de se identificar padrões de interação entre os vários grupos de bactérias presentes em solos ornitogênicos em diferentes profundidades (camadas). A análise das sequências revelou a presença de oito filos distribuídos em diferentes proporções entre as Camadas 1 (0-8 cm), 2 (20-25 cm) e 3 (35-40 cm). De acordo com os índices de diversidade, a Camada 3 apresentou os maiores valores de riqueza, diversidade e uniformidade quando comparado com as Camadas 1 e 2.
  • Discovered by Genomics Putative Reductive Dehalogenases with N-Terminus Transmembrane Helixes

    Discovered by Genomics Putative Reductive Dehalogenases with N-Terminus Transmembrane Helixes

    Discovered by genomics putative reductive dehalogenases with N-terminus transmembrane helixes Atashgahi, S. This is a "Post-Print" accepted manuscript, which has been published in "FEMS microbiology ecology" This version is distributed under a non-commercial no derivatives Creative Commons (CC-BY-NC-ND) user license, which permits use, distribution, and reproduction in any medium, provided the original work is properly cited and not used for commercial purposes. Further, the restriction applies that if you remix, transform, or build upon the material, you may not distribute the modified material. Please cite this publication as follows: Atashgahi, S. (2019). Discovered by genomics putative reductive dehalogenases with N-terminus transmembrane helixes. FEMS microbiology ecology, 95(5), [fiz048]. https://doi.org/10.1093/femsec/fiz048 1 Discovered by genomics: Putative reductive dehalogenases with N-terminus 2 transmembrane helixes 3 Siavash Atashgahi 1,2,3 4 1 Laboratory of Microbiology, Wageningen University & Research, Wageningen, The 5 Netherlands 6 2 Department of Microbiology, Radboud University, Nijmegen, The Netherlands 7 3 Soehngen Institute of Anaerobic Microbiology, Nijmegen, The Netherlands 8 [email protected]; [email protected]; http://orcid.org/0000-0002-2793- 9 2321; +31243652564 10 11 Abstract 12 Attempts for bioremediation of toxic organohalogens resulted in the identification 13 of organohalide-respiring bacteria harbouring reductive dehalogenases (RDases) enzymes. 14 RDases consist of the catalytic subunit (RdhA, encoded by rdhA) that does not have 15 membrane-integral domains, and a small putative membrane anchor (RdhB, encoded by 16 rdhB) that (presumably) locates the A subunit to the outside of the cytoplasmic membrane. 17 Recent genomic studies identified a putative rdh gene in an uncultured deltaproteobacterial 18 genome that was not accompanied by an rdhB gene, but contained transmembrane helixes 19 in N-terminus.
  • Roseibacterium Beibuensis Sp. Nov., a Novel Member of Roseobacter Clade Isolated from Beibu Gulf in the South China Sea

    Roseibacterium Beibuensis Sp. Nov., a Novel Member of Roseobacter Clade Isolated from Beibu Gulf in the South China Sea

    Curr Microbiol (2012) 65:568–574 DOI 10.1007/s00284-012-0192-6 Roseibacterium beibuensis sp. nov., a Novel Member of Roseobacter Clade Isolated from Beibu Gulf in the South China Sea Yujiao Mao • Jingjing Wei • Qiang Zheng • Na Xiao • Qipei Li • Yingnan Fu • Yanan Wang • Nianzhi Jiao Received: 6 April 2012 / Accepted: 25 June 2012 / Published online: 31 July 2012 Ó Springer Science+Business Media, LLC 2012 Abstract A novel aerobic, bacteriochlorophyll-contain- similarity), followed by Dinoroseobacter shibae DFL 12T ing bacteria strain JLT1202rT was isolated from Beibu Gulf (95.4 % similarity). The phylogenetic distance of pufM genes in the South China Sea. Cells were gram-negative, non- between strain JLT1202rT and R. elongatum OCh 323T was motile, and short-ovoid to rod-shaped with two narrower 9.4 %, suggesting that strain JLT1202rT was distinct from the poles. Strain JLT1202rT formed circular, opaque, wine-red only strain of the genus Roseibacterium. Based on the vari- colonies, and grew optimally at 3–4 % NaCl, pH 7.5–8.0 abilities of phylogenetic and phenotypic characteristics, strain and 28–30 °C. The strain was catalase, oxidase, ONPG, JLT1202rT stands for a novel species of the genus Roseibac- gelatin, and Voges–Proskauer test positive. In vivo terium and the name R. beibuensis sp. nov. is proposed with absorption spectrum of bacteriochlorophyll a presented two JLT1202rT as the type strain (=JCM 18015T = CGMCC peaks at 800 and 877 nm. The predominant cellular fatty 1.10994T). acid was C18:1 x7c and significant amounts of C16:0,C18:0, C10:0 3-OH, C16:0 2-OH, and 11-methyl C18:1 x7c were present.
  • Microbial Diversity Under Extreme Euxinia: Mahoney Lake, Canada V

    Microbial Diversity Under Extreme Euxinia: Mahoney Lake, Canada V

    Geobiology (2012), 10, 223–235 DOI: 10.1111/j.1472-4669.2012.00317.x Microbial diversity under extreme euxinia: Mahoney Lake, Canada V. KLEPAC-CERAJ,1,2 C. A. HAYES,3 W. P. GILHOOLY,4 T. W. LYONS,5 R. KOLTER2 AND A. PEARSON3 1Department of Molecular Genetics, Forsyth Institute, Cambridge, MA, USA 2Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA, USA 3Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, USA 4Department of Earth and Planetary Sciences, Washington University, Saint Louis, MO, USA 5Department of Earth Sciences, University of California, Riverside, CA, USA ABSTRACT Mahoney Lake, British Columbia, Canada, is a stratified, 15-m deep saline lake with a euxinic (anoxic, sulfidic) hypolimnion. A dense plate of phototrophic purple sulfur bacteria is found at the chemocline, but to date the rest of the Mahoney Lake microbial ecosystem has been underexamined. In particular, the microbial community that resides in the aphotic hypolimnion and ⁄ or in the lake sediments is unknown, and it is unclear whether the sulfate reducers that supply sulfide for phototrophy live only within, or also below, the plate. Here we profiled distribu- tions of 16S rRNA genes using gene clone libraries and PhyloChip microarrays. Both approaches suggest that microbial diversity is greatest in the hypolimnion (8 m) and sediments. Diversity is lowest in the photosynthetic plate (7 m). Shallower depths (5 m, 7 m) are rich in Actinobacteria, Alphaproteobacteria, and Gammaproteo- bacteria, while deeper depths (8 m, sediments) are rich in Crenarchaeota, Natronoanaerobium, and Verrucomi- crobia. The heterogeneous distribution of Deltaproteobacteria and Epsilonproteobacteria between 7 and 8 m is consistent with metabolisms involving sulfur intermediates in the chemocline, but complete sulfate reduction in the hypolimnion.
  • Bacterial Avidins Are a Widely Distributed Protein Family in Actinobacteria, Proteobacteria and Bacteroidetes Olli H

    Bacterial Avidins Are a Widely Distributed Protein Family in Actinobacteria, Proteobacteria and Bacteroidetes Olli H

    Laitinen et al. BMC Ecol Evo (2021) 21:53 BMC Ecology and Evolution https://doi.org/10.1186/s12862-021-01784-y RESEARCH ARTICLE Open Access Bacterial avidins are a widely distributed protein family in Actinobacteria, Proteobacteria and Bacteroidetes Olli H. Laitinen1†, Tanja P. Kuusela1†, Sampo Kukkurainen1†, Anssi Nurminen1, Aki Sinkkonen2 and Vesa P. Hytönen1,3* Abstract Background: Avidins are biotin-binding proteins commonly found in the vertebrate eggs. In addition to streptavidin from Streptomyces avidinii, a growing number of avidins have been characterized from divergent bacterial species. However, a systematic research concerning their taxonomy and ecological role has never been done. We performed a search for avidin encoding genes among bacteria using available databases and classifed potential avidins according to taxonomy and the ecological niches utilized by host bacteria. Results: Numerous avidin-encoding genes were found in the phyla Actinobacteria and Proteobacteria. The diversity of protein sequences was high and several new variants of genes encoding biotin-binding avidins were found. The living strategies of bacteria hosting avidin encoding genes fall mainly into two categories. Human and animal patho- gens were overrepresented among the found bacteria carrying avidin genes. The other widespread category were bacteria that either fx nitrogen or live in root nodules/rhizospheres of plants hosting nitrogen-fxing bacteria. Conclusions: Bacterial avidins are a taxonomically and ecologically diverse group mainly found in Actinobacteria, Proteobacteria and Bacteroidetes, associated often with plant invasiveness. Avidin encoding genes in plasmids hint that avidins may be horizontally transferred. The current survey may be used as a basis in attempts to understand the ecological signifcance of biotin-binding capacity.
  • Dissertation Implementing Organic Amendments To

    Dissertation Implementing Organic Amendments To

    DISSERTATION IMPLEMENTING ORGANIC AMENDMENTS TO ENHANCE MAIZE YIELD, SOIL MOISTURE, AND MICROBIAL NUTRIENT CYCLING IN TEMPERATE AGRICULTURE Submitted by Erika J. Foster Graduate Degree Program in Ecology In partial fulfillment of the requirements For the Degree of Doctor of Philosophy Colorado State University Fort Collins, Colorado Summer 2018 Doctoral Committee: Advisor: M. Francesca Cotrufo Louise Comas Charles Rhoades Matthew D. Wallenstein Copyright by Erika J. Foster 2018 All Rights Reserved i ABSTRACT IMPLEMENTING ORGANIC AMENDMENTS TO ENHANCE MAIZE YIELD, SOIL MOISTURE, AND MICROBIAL NUTRIENT CYCLING IN TEMPERATE AGRICULTURE To sustain agricultural production into the future, management should enhance natural biogeochemical cycling within the soil. Strategies to increase yield while reducing chemical fertilizer inputs and irrigation require robust research and development before widespread implementation. Current innovations in crop production use amendments such as manure and biochar charcoal to increase soil organic matter and improve soil structure, water, and nutrient content. Organic amendments also provide substrate and habitat for soil microorganisms that can play a key role cycling nutrients, improving nutrient availability for crops. Additional plant growth promoting bacteria can be incorporated into the soil as inocula to enhance soil nutrient cycling through mechanisms like phosphorus solubilization. Since microbial inoculation is highly effective under drought conditions, this technique pairs well in agricultural systems using limited irrigation to save water, particularly in semi-arid regions where climate change and population growth exacerbate water scarcity. The research in this dissertation examines synergistic techniques to reduce irrigation inputs, while building soil organic matter, and promoting natural microbial function to increase crop available nutrients. The research was conducted on conventional irrigated maize systems at the Agricultural Research Development and Education Center north of Fort Collins, CO.
  • Bacterial Community Change Through Drinking Water Treatment Processes

    Bacterial Community Change Through Drinking Water Treatment Processes

    Int. J. Environ. Sci. Technol. (2015) 12:1867–1874 DOI 10.1007/s13762-014-0540-0 ORIGINAL PAPER Bacterial community change through drinking water treatment processes X. Liao • C. Chen • Z. Wang • C.-H. Chang • X. Zhang • S. Xie Received: 28 August 2012 / Revised: 30 September 2013 / Accepted: 5 March 2014 / Published online: 18 March 2014 Ó Islamic Azad University (IAU) 2014 Abstract The microbiological quality of drinking water Introduction has aroused increasing attention due to potential public health risks. Knowledge of the bacterial ecology in the The microbiological quality of drinking water has aroused effluents of drinking water treatment units will be of practical increasing attention due to potential public health risks. importance. However, the bacterial community in the The conventional treatment process, composed of coagu- effluents of drinking water filters remains poorly understood. lation–flocculation, sedimentation, rapid sand filtration, The changes of the density of viable heterotrophic bacteria and disinfection, is still widely used by drinking water and bacterial populations through a pilot-scale drinking producers to remove turbidity and pathogens. The con- water treatment process were investigated using heterotro- ventional treatment process is not efficient in removal of phic plate counts and clone library analysis, respectively. biodegradable dissolved organic carbon (BDOC) that is The pilot-scale treatment process was composed of preozo- mainly responsible for the microbial regrowth in drinking nation, rapid mixing, flocculation, sedimentation, sand fil- water distribution systems (DWDS). Biological activated tration postozonation, and biological activated carbon carbon (BAC) filtration can perform well in reduction of (BAC) filtration. The results indicated that heterotrophic organic pollutants after the attachment of the indigenous plate counts decreased dramatically through the drinking microbiota attached to the porous surface of granular water treatment processes.
  • Influencia De La Comunidad Bacteriana En Los Ciclos Biogeoquímicos Del Carbono Y El Nitrógeno En El Ecosistema De Manglar

    Influencia De La Comunidad Bacteriana En Los Ciclos Biogeoquímicos Del Carbono Y El Nitrógeno En El Ecosistema De Manglar

    FACULTAD CIENCIAS DE LA SALUD BACTERIOLOGÍA Y LABORATORIO CLÍNICO BOGOTÁ D.C. 2020 Proyecto: INFLUENCIA DE LA COMUNIDAD BACTERIANA EN LOS CICLOS BIOGEOQUÍMICOS DEL CARBONO Y EL NITRÓGENO EN EL ECOSISTEMA DE MANGLAR Meritoria: _____Si______ Laureada: ___________ Aprobada: ___________ JURADOS _____________________ ________________ ____________________ _________________ _________________________________________________ ASESOR(es) _________ Martha Lucía Posada Buitrago___________________ _________________________________________ ÉTICA, SERVICIO Y SABER INFLUENCIA DE LA COMUNIDAD BACTERIANA EN LOS CICLOS BIOGEOQUÍMICOS DEL CARBONO Y EL NITRÓGENO EN EL ECOSISTEMA DE MANGLAR UNIVERSIDAD COLEGIO MAYOR DE CUNDINAMARCA FACULTAD CIENCIAS DE LA SALUD PROGRAMA BACTERIOLOGÍA Y LABORATORIO CLÍNICO PROYECTO DE GRADO BOGOTÁ D.C 2020 INFLUENCIA DE LA COMUNIDAD BACTERIANA EN LOS CICLOS BIOGEOQUÍMICOS DEL CARBONO Y EL NITRÓGENO EN EL ECOSISTEMA DE MANGLAR Danya Gabriela Ramírez Lozada Nicolás David Rojas Villamil Asesor interno PhD. Martha Lucía Posada Buitrago Monografía para optar al título de Bacteriólogo y Laboratorista Clínico UNIVERSIDAD COLEGIO MAYOR DE CUNDINAMARCA FACULTAD CIENCIAS DE LA SALUD PROGRAMA BACTERIOLOGÍA Y LABORATORIO CLÍNICO PROYECTO DE GRADO BOGOTÁ D.C 2020 INFLUENCIA DE LA COMUNIDAD BACTERIANA EN LOS CICLOS BIOGEOQUÍMICOS DEL CARBONO Y EL NITRÓGENO EN EL ECOSISTEMA DE MANGLAR UNIVERSIDAD COLEGIO MAYOR DE CUNDINAMARCA FACULTAD CIENCIAS DE LA SALUD PROGRAMA BACTERIOLOGÍA Y LABORATORIO CLÍNICO PROYECTO DE GRADO BOGOTÁ D.C 2020 DEDICATORIA A todas las personas y docentes que hicieron parte de nuestro proceso de formación profesional, a nuestras familias y amigos, que nos brindaron su apoyo, tiempo, consejos y paciencia en este camino que no ha culminado y aún está lleno de sueños, esperanzas y metas por alcanzar. AGRADECIMIENTOS Principalmente a nuestras familias porque han sido la base de nuestra formación aportando grandes cosas en nuestras vidas, por confiar y creer en nuestras capacidades y destrezas a lo largo de esta carrera.
  • Limibaculum Halophilum Gen. Nov., Sp. Nov., a New Member of the Family Rhodobacteraceae

    Limibaculum Halophilum Gen. Nov., Sp. Nov., a New Member of the Family Rhodobacteraceae

    TAXONOMIC DESCRIPTION Shin et al., Int J Syst Evol Microbiol 2017;67:3812–3818 DOI 10.1099/ijsem.0.002200 Limibaculum halophilum gen. nov., sp. nov., a new member of the family Rhodobacteraceae Yong Ho Shin,1 Jong-Hwa Kim,1 Ampaitip Suckhoom,2 Duangporn Kantachote2 and Wonyong Kim1,* Abstract A Gram-stain-negative, cream-pigmented, aerobic, non-motile, non-spore-forming and short-rod-shaped bacterial strain, designated CAU 1123T, was isolated from mud from reclaimed land. The strain’s taxonomic position was investigated by using a polyphasic approach. Strain CAU 1123T grew optimally at 37 C and at pH 7.5 in the presence of 2 % (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain CAU 1123T formed a monophyletic lineage within the family Rhodobacteraceae with 93.8 % or lower sequence similarity to representatives of the genera Rubrimonas, Oceanicella, Pleomorphobacterium, Rhodovulum and Albimonas. The major fatty acids were C18 : 1 !7c and 11-methyl C18 : 1 !7c and the predominant respiratory quinone was Q-10. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, two unidentified phospholipids, one unidentified aminolipid and one unidentified lipid. The DNA G+C content was 71.1 mol%. Based on the data from phenotypic, chemotaxonomic and phylogenetic studies, it is proposed that strain CAU 1123T represents a novel genus and novel species of the family Rhodobacteraceae, for which the name Limibaculumhalophilum gen. nov., sp. nov. The type strain is CAU 1123T (=KCTC 52187T, =NBRC 112522T). The family Rhodobacteraceae was first established by Garr- chemotaxonomic properties along with a detailed phyloge- ity et al.