Accepted Article
Received Date : 29-Jan-2014 Revised Date : 29-Apr-2014 Accepted Date : 11-May-2014 Article type : Research Paper Editor : Johanna Laybourn-Parry
Spatial biodiversity of bacteria along the largest Arctic river determined by next-generation sequencing Olesya V Kolmakova1,2,* , Michail I Gladyshev1,2, Alexey S Rozanov3, Sergey E Peltek3, Maria Y Trusova2 1
Siberian Federal University, Krasnoyarsk, Russia
2
Institute of Biophysics of Siberian Branch of Russian Academy of Sciences,
Krasnoyarsk, Russia 3
Institute of Cytology & Genetics of Siberian Branch of Russian Academy of Sciences,
Novosibirsk, Russia Keywords: bacterial community; the Yenisei River; 16S rRNA; diversity. Running title: NGS of the Yenisei River bacterioplankton Corresponding author. Address: Institute of Biophysics, 50/50 Akademgorodok, 660036 Krasnoyarsk, Russia. Tel.: (+7) 9509817601, fax: (+7) 3912433400, e-mail: [email protected]
Abstract Biodiversity of bacterial communities along the Yenisei River at section ~1800 km was studied using next-generation sequencing of 16S rRNA genes and common biodiversity indices. Overall 3022 unique operational taxonomic units were identified. Actinobacteria and Proteobacteria were dominant phyla at all sampling sites. The highest alpha-diversity values were found in the middle section of the studied river. Beta-diversity of bacterial assemblages in the river was related with surrounding landscape (biome): three distinctly different bacterial assemblages occurred in sections of the river, situated in mountain taiga, plain taiga and in region of permafrost, covered by forest-tundra and tundra. Tributaries, arisen from these This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as doi: 10.1111/1574-6941.12355 This article is protected by copyright. All rights reserved.
Accepted Article
different landscapes, likely contributed substantially to the variations of Yenisei bacterial communities. In contrast to a prediction of the river continuum concept, proportion of photoautotrophic Cyanobacteria in bacterial assemblages did not increase downstream the river, but peaked at the middle section. Introduction Recently rivers were found to be the main source of global carbon dioxide emission from inland waters, in spite of their comparatively small surface area (Raymond et al., 2013; Ward et al., 2013). Thus, rivers already are not regarded as ‘passive pipes’ which only transport carbon from land to sea, but are recognized as active components of the global C cycle which store and respire terrestrially-derived organic matter (Cole et al., 2007). As a parcel of organic matter moves through the river continuum, it is primarily degraded by microbial activity. However, our present understanding of microbial controls of the organic matter pool is speculative at best (Ward et al., 2013). Since each microbial species carries out its own specific ‘biogeochemical work’ (Vernadsky, 1978), in order to unravel and quantify roles of aquatic microorganisms in carbon cycles, we need to know their species composition first of all. Nevertheless, at present surprisingly little is known about species diversity of river bacterial communities (Schultz et al., 2013). In available literature, there are few studies of microbial community composition and diversity in rivers based on technology of next-generation sequencing (NGS) (Fortunato et al., 2012; Ghai et al., 2011; Schultz et al., 2013; Staley et al, 2013). Evidently, significantly more studies are needed to determine the bacterial diversity and community structure contained within rivers (Schultz et al., 2013). Moreover, the above studies comprised only one site or a short section of the rivers (Fortunato et al., 2012; Ghai et al., 2011; Schultz et al., 2013, Staley et al, 2013), and thereby were not aimed to reveal any patterns of distribution of microbial biodiversity downstream the rivers. Thus, we make the first known attempt using
This article is protected by copyright. All rights reserved.
Accepted Article
next-generation sequencing to describe bacterial biodiversity in the great world river, Yenisei, along a section of about 2000 km. Pioneering work on molecular genetic analysis of diversity of Yenisei bacterioplankton was carried out by Crump et al. (2009) in a lower section of the river near estuary basing on methods of previous generation. The studied Yenisei River is the largest Arctic river in terms of discharge of dissolved and particulate organic carbon, 4.5 · 1012 g · year-1 and 0.2 · 1012 g · year-1, respectively (Dittmar & Kattner, 2003). Contribution of specific sections of the river, situated in diverse landscapes, to this integral discharge may be different. Quantitative and qualitative contributions of specific river sections to the globally important carbon discharge of the Yenisei River likely depends on peculiarities of inputs of allochthonous organic matter from surrounding landscape and on traits of river microbial communities, including species composition and diversity, which control the organic matter pool. We intended testing two main hypotheses: 1) alpha-diversity monotonously increased downstream the river; 2) betadiversity in the river is shaped by surrounding landscape (biome). Additionally, we aimed to verify the finding of Schultz et al. (2013) that proportion of Cyanobacteria in prokaryotic assemblages increased downstream according to river continuum concept. Materials and Methods Water samples were collected from the Yenisei River, which is the longest river (4803 km) and has the greatest discharge (636 km3 yr-1) among all the rivers, flowing into the Arctic Ocean (Amon et al., 2012). Detailed information about the ecological characteristics of the river is given elsewhere (Telang et al., 1991). Briefly, its main hydrochemical features are low turbidity (
Received Date : 29-Jan-2014 Revised Date : 29-Apr-2014 Accepted Date : 11-May-2014 Article type : Research Paper Editor : Johanna Laybourn-Parry
Spatial biodiversity of bacteria along the largest Arctic river determined by next-generation sequencing Olesya V Kolmakova1,2,* , Michail I Gladyshev1,2, Alexey S Rozanov3, Sergey E Peltek3, Maria Y Trusova2 1
Siberian Federal University, Krasnoyarsk, Russia
2
Institute of Biophysics of Siberian Branch of Russian Academy of Sciences,
Krasnoyarsk, Russia 3
Institute of Cytology & Genetics of Siberian Branch of Russian Academy of Sciences,
Novosibirsk, Russia Keywords: bacterial community; the Yenisei River; 16S rRNA; diversity. Running title: NGS of the Yenisei River bacterioplankton Corresponding author. Address: Institute of Biophysics, 50/50 Akademgorodok, 660036 Krasnoyarsk, Russia. Tel.: (+7) 9509817601, fax: (+7) 3912433400, e-mail: [email protected]
Abstract Biodiversity of bacterial communities along the Yenisei River at section ~1800 km was studied using next-generation sequencing of 16S rRNA genes and common biodiversity indices. Overall 3022 unique operational taxonomic units were identified. Actinobacteria and Proteobacteria were dominant phyla at all sampling sites. The highest alpha-diversity values were found in the middle section of the studied river. Beta-diversity of bacterial assemblages in the river was related with surrounding landscape (biome): three distinctly different bacterial assemblages occurred in sections of the river, situated in mountain taiga, plain taiga and in region of permafrost, covered by forest-tundra and tundra. Tributaries, arisen from these This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as doi: 10.1111/1574-6941.12355 This article is protected by copyright. All rights reserved.
Accepted Article
different landscapes, likely contributed substantially to the variations of Yenisei bacterial communities. In contrast to a prediction of the river continuum concept, proportion of photoautotrophic Cyanobacteria in bacterial assemblages did not increase downstream the river, but peaked at the middle section. Introduction Recently rivers were found to be the main source of global carbon dioxide emission from inland waters, in spite of their comparatively small surface area (Raymond et al., 2013; Ward et al., 2013). Thus, rivers already are not regarded as ‘passive pipes’ which only transport carbon from land to sea, but are recognized as active components of the global C cycle which store and respire terrestrially-derived organic matter (Cole et al., 2007). As a parcel of organic matter moves through the river continuum, it is primarily degraded by microbial activity. However, our present understanding of microbial controls of the organic matter pool is speculative at best (Ward et al., 2013). Since each microbial species carries out its own specific ‘biogeochemical work’ (Vernadsky, 1978), in order to unravel and quantify roles of aquatic microorganisms in carbon cycles, we need to know their species composition first of all. Nevertheless, at present surprisingly little is known about species diversity of river bacterial communities (Schultz et al., 2013). In available literature, there are few studies of microbial community composition and diversity in rivers based on technology of next-generation sequencing (NGS) (Fortunato et al., 2012; Ghai et al., 2011; Schultz et al., 2013; Staley et al, 2013). Evidently, significantly more studies are needed to determine the bacterial diversity and community structure contained within rivers (Schultz et al., 2013). Moreover, the above studies comprised only one site or a short section of the rivers (Fortunato et al., 2012; Ghai et al., 2011; Schultz et al., 2013, Staley et al, 2013), and thereby were not aimed to reveal any patterns of distribution of microbial biodiversity downstream the rivers. Thus, we make the first known attempt using
This article is protected by copyright. All rights reserved.
Accepted Article
next-generation sequencing to describe bacterial biodiversity in the great world river, Yenisei, along a section of about 2000 km. Pioneering work on molecular genetic analysis of diversity of Yenisei bacterioplankton was carried out by Crump et al. (2009) in a lower section of the river near estuary basing on methods of previous generation. The studied Yenisei River is the largest Arctic river in terms of discharge of dissolved and particulate organic carbon, 4.5 · 1012 g · year-1 and 0.2 · 1012 g · year-1, respectively (Dittmar & Kattner, 2003). Contribution of specific sections of the river, situated in diverse landscapes, to this integral discharge may be different. Quantitative and qualitative contributions of specific river sections to the globally important carbon discharge of the Yenisei River likely depends on peculiarities of inputs of allochthonous organic matter from surrounding landscape and on traits of river microbial communities, including species composition and diversity, which control the organic matter pool. We intended testing two main hypotheses: 1) alpha-diversity monotonously increased downstream the river; 2) betadiversity in the river is shaped by surrounding landscape (biome). Additionally, we aimed to verify the finding of Schultz et al. (2013) that proportion of Cyanobacteria in prokaryotic assemblages increased downstream according to river continuum concept. Materials and Methods Water samples were collected from the Yenisei River, which is the longest river (4803 km) and has the greatest discharge (636 km3 yr-1) among all the rivers, flowing into the Arctic Ocean (Amon et al., 2012). Detailed information about the ecological characteristics of the river is given elsewhere (Telang et al., 1991). Briefly, its main hydrochemical features are low turbidity (
