Environmental Microbiology Microbiology (2016) (2015) 18(6), 1782–1791
doi:10.1111/1462-2920.12938 doi:10.1111/1462-2920.12938
Microbial diversity and community structure along a lake elevation gradient in Yosemite National Park, California, USA
Curtis J. Hayden and J. Michael Beman* Life and Environmental Sciences and Sierra Nevada Research Institute, University of California, Merced, California 95343, USA. Summary Microbial communities are key components of lake ecosystems and play central roles in lake biogeochemical cycles. Freshwater lakes, in turn, have a disproportionate influence on global carbon and nitrogen cycling, while also acting as ‘sentinels’ of environmental change. Determining what factors regulate microbial community dynamics and their relationship to lake biogeochemistry is therefore essential to understanding global change feedbacks. We used ILLUMINA sequencing of >2 million 16S rRNA genes to examine microbial community structure and diversity in relation to spatial, temporal and biogeochemical variation, within and across lakes located along a 871 m elevation gradient in Yosemite National Park, California, USA. We captured a rich microbial community that included many rare operational taxonomic units (OTUs), but was dominated by a few bacterial classes and OTUs frequently detected in other freshwater ecosystems. Neither richness, evenness nor overall diversity was directly related to elevation. However, redundancy analysis showed that changes in microbial community structure were significantly related to elevation. Along with sampling period and dissolved nutrient concentrations, 29% of the variation in community structure could be explained by measured variables – in congruence with studies in other lakes using different techniques. We also found a distance–decay relationship in microbial community structure across lakes, suggesting that both local environmental factors and dispersal play a role in structuring communities.
Received 2 October, 2014; revised 12 May, 2015; accepted 17 May, 2015. *For correspondence. E-mail [email protected]; Tel. +(650) 823-7925; Fax +209-228-4713. C 2015 Society for © for Applied Applied Microbiology Microbiology and and John John Wiley Wiley && Sons Sons Ltd Ltd V
Introduction Lakes receive and process large volumes of material within their watersheds, functioning as biogeochemical integrators of the surrounding landscape (Williamson et al., 2009). Lakes therefore have a disproportionate influence on global biogeochemical cycles of carbon (C) and nitrogen (N) (Cole et al., 2007; Finlay et al., 2013), and they are also ‘sentinel’ ecosystems that can be rapidly and substantially altered by global change (Tranvik et al., 2009). Within lakes, microbial communities play a central role in controlling C and N cycling, yet variations in lake microbial diversity and composition are still understudied (Newton et al., 2011). ‘Typical’ freshwater bacteria and their phenology were identified only in the past decade (Zwart et al., 2002; Shade et al., 2007; Nelson, 2009), and it is obviously challenging to test for the universality of these patterns in the 117 million lakes found across the globe (Verpoorter et al., 2014). Approximately 10% of all lakes are located above 2000 m in elevation (Verpoorter et al., 2014), with thousands of high-elevation lakes found in the Sierra Nevada mountain range, California, USA. These lakes are typically oligotrophic (Sickman et al., 2003), and so microbial communities are particularly influential due to low productivity and an active microbial loop (Cotner and Biddanda, 2002). Yet high-elevation regions are expected to rapidly warm (Beniston et al., 1997), and can experience elevated levels of pollution that are concentrated at high altitudes (Clow et al., 2010; Baron et al., 2013). In macrobial ecology, elevation gradients are a common ‘space for time’ substitution used to examine the potential effects of such changes (Sundqvist et al., 2013). Elevation gradients have been used in Yosemite National Park in the Sierra Nevada, CA, for instance, to examine the effects of climate change on animal populations and communities (Moritz et al., 2008). Beyond their application to climate change, elevation gradients have well-known biogeographical effects on communities of large organisms, which typically show maximum diversity at mid-elevation or at low elevation (Sundqvist et al., 2013). Many of the environmental factors that vary with elevation could affect individual microbes and therefore overall microbial diversity along elevation gradients; for example, these factors
2
Lake microbial ecology along an elevation gradient 1783
C. J. Hayden and J. M. Beman
A
0
8
16
24
32 km
B Elevation (m)
3200 3000 2800 2600 2400 2200 119.25˚
Temperature (˚C)
C
119.35
119.45˚ 119.55˚ Longitude (˚W)
119.65˚
119.75˚
24
We examined lake microbial communities along an elevation gradient in Yosemite National Park, sampling 15 lakes that span 2289–3160 m elevation (Fig. 1). Nine lakes were also sampled multiple times to account for temporal changes in microbial communities from early to mid to late summer. We used high-throughput ILLUMINA sequencing of 16S rRNA genes to examine microbial community ecology, and to determine to what degree variations in microbial community structure and diversity are related to spatio-temporal and environmental variation. Spatial patterns of macrobiota have been documented across many habitat types, and these patterns of diversity are beginning to be unraveled for microbial communities (Martiny et al., 2006). There is evidence that, in some cases, microbes follow classic ecological patterns (e.g. latitudinal gradients, taxa–area relationships, distance–decay relationships and co-occurrence patterns) (Fuhrman, 2009; Soininen, 2012), and that these patterns are driven by both deterministic (or niche/ selective) processes as well as stochastic (or neutral/ ‘drift’) processes (Hanson et al., 2012). For example, earlier work in the Sierra Nevada, USA provides support for within-lake environmental selection (Nelson et al., 2009), while a regional scale study of high-elevation lake systems in the Sierra Nevada, Spain found that geographic distance between lakes was the primary determinant of bacterial community composition (Reche et al., 2005; but see Lindström et al., 2007). We used a variety of statistical approaches to examine microbial community assembly in high-altitude lakes.
Results and discussion
21
Variations in microbial community structure across and within lakes
18 15 12 2200
2400
2800 2600 Elevation (m)
3000
3200
Fig. 1. A. Map of sampled lakes on 10 m resolution elevation data of Yosemite National Park from the United States Geological Survey National Elevation Dataset (http://nationalmap.gov/). B. Lake elevation plotted against lake longitude. C. Lake temperature plotted against lake elevation for lakes sampled in July (white data points) and in August/September (black data points). In addition to temperature, multiple other environmental factors are expected to vary with elevation.
include temperature, UV radiation, atmospheric deposition of nutrients and primary production. However, several studies have examined elevational patterns in microbial diversity and community structure with mixed results: some detect significant trends (Bryant et al., 2008; Wang et al., 2012), while others do not (Fierer et al., 2011).
High-altitude lakes were frequently dominated by freshwater bacteria observed in previous studies, although the relative proportions of these groups varied across lakes and over time within individual lakes. Six bacterial phyla made up the vast majority of >2 million total 16S rRNA sequences: Proteobacteria (>730 000 sequences), Actinobacteria (>715 000 sequences), Bacteroidetes (>324 600 sequences), Verrucomibcrobia (>176 000 sequences), Cyanobacteria (>55 800 sequences) and Planctomycetes (>15 800 sequences) (Fig. 2). The remaining phyla made up
doi:10.1111/1462-2920.12938 doi:10.1111/1462-2920.12938
Microbial diversity and community structure along a lake elevation gradient in Yosemite National Park, California, USA
Curtis J. Hayden and J. Michael Beman* Life and Environmental Sciences and Sierra Nevada Research Institute, University of California, Merced, California 95343, USA. Summary Microbial communities are key components of lake ecosystems and play central roles in lake biogeochemical cycles. Freshwater lakes, in turn, have a disproportionate influence on global carbon and nitrogen cycling, while also acting as ‘sentinels’ of environmental change. Determining what factors regulate microbial community dynamics and their relationship to lake biogeochemistry is therefore essential to understanding global change feedbacks. We used ILLUMINA sequencing of >2 million 16S rRNA genes to examine microbial community structure and diversity in relation to spatial, temporal and biogeochemical variation, within and across lakes located along a 871 m elevation gradient in Yosemite National Park, California, USA. We captured a rich microbial community that included many rare operational taxonomic units (OTUs), but was dominated by a few bacterial classes and OTUs frequently detected in other freshwater ecosystems. Neither richness, evenness nor overall diversity was directly related to elevation. However, redundancy analysis showed that changes in microbial community structure were significantly related to elevation. Along with sampling period and dissolved nutrient concentrations, 29% of the variation in community structure could be explained by measured variables – in congruence with studies in other lakes using different techniques. We also found a distance–decay relationship in microbial community structure across lakes, suggesting that both local environmental factors and dispersal play a role in structuring communities.
Received 2 October, 2014; revised 12 May, 2015; accepted 17 May, 2015. *For correspondence. E-mail [email protected]; Tel. +(650) 823-7925; Fax +209-228-4713. C 2015 Society for © for Applied Applied Microbiology Microbiology and and John John Wiley Wiley && Sons Sons Ltd Ltd V
Introduction Lakes receive and process large volumes of material within their watersheds, functioning as biogeochemical integrators of the surrounding landscape (Williamson et al., 2009). Lakes therefore have a disproportionate influence on global biogeochemical cycles of carbon (C) and nitrogen (N) (Cole et al., 2007; Finlay et al., 2013), and they are also ‘sentinel’ ecosystems that can be rapidly and substantially altered by global change (Tranvik et al., 2009). Within lakes, microbial communities play a central role in controlling C and N cycling, yet variations in lake microbial diversity and composition are still understudied (Newton et al., 2011). ‘Typical’ freshwater bacteria and their phenology were identified only in the past decade (Zwart et al., 2002; Shade et al., 2007; Nelson, 2009), and it is obviously challenging to test for the universality of these patterns in the 117 million lakes found across the globe (Verpoorter et al., 2014). Approximately 10% of all lakes are located above 2000 m in elevation (Verpoorter et al., 2014), with thousands of high-elevation lakes found in the Sierra Nevada mountain range, California, USA. These lakes are typically oligotrophic (Sickman et al., 2003), and so microbial communities are particularly influential due to low productivity and an active microbial loop (Cotner and Biddanda, 2002). Yet high-elevation regions are expected to rapidly warm (Beniston et al., 1997), and can experience elevated levels of pollution that are concentrated at high altitudes (Clow et al., 2010; Baron et al., 2013). In macrobial ecology, elevation gradients are a common ‘space for time’ substitution used to examine the potential effects of such changes (Sundqvist et al., 2013). Elevation gradients have been used in Yosemite National Park in the Sierra Nevada, CA, for instance, to examine the effects of climate change on animal populations and communities (Moritz et al., 2008). Beyond their application to climate change, elevation gradients have well-known biogeographical effects on communities of large organisms, which typically show maximum diversity at mid-elevation or at low elevation (Sundqvist et al., 2013). Many of the environmental factors that vary with elevation could affect individual microbes and therefore overall microbial diversity along elevation gradients; for example, these factors
2
Lake microbial ecology along an elevation gradient 1783
C. J. Hayden and J. M. Beman
A
0
8
16
24
32 km
B Elevation (m)
3200 3000 2800 2600 2400 2200 119.25˚
Temperature (˚C)
C
119.35
119.45˚ 119.55˚ Longitude (˚W)
119.65˚
119.75˚
24
We examined lake microbial communities along an elevation gradient in Yosemite National Park, sampling 15 lakes that span 2289–3160 m elevation (Fig. 1). Nine lakes were also sampled multiple times to account for temporal changes in microbial communities from early to mid to late summer. We used high-throughput ILLUMINA sequencing of 16S rRNA genes to examine microbial community ecology, and to determine to what degree variations in microbial community structure and diversity are related to spatio-temporal and environmental variation. Spatial patterns of macrobiota have been documented across many habitat types, and these patterns of diversity are beginning to be unraveled for microbial communities (Martiny et al., 2006). There is evidence that, in some cases, microbes follow classic ecological patterns (e.g. latitudinal gradients, taxa–area relationships, distance–decay relationships and co-occurrence patterns) (Fuhrman, 2009; Soininen, 2012), and that these patterns are driven by both deterministic (or niche/ selective) processes as well as stochastic (or neutral/ ‘drift’) processes (Hanson et al., 2012). For example, earlier work in the Sierra Nevada, USA provides support for within-lake environmental selection (Nelson et al., 2009), while a regional scale study of high-elevation lake systems in the Sierra Nevada, Spain found that geographic distance between lakes was the primary determinant of bacterial community composition (Reche et al., 2005; but see Lindström et al., 2007). We used a variety of statistical approaches to examine microbial community assembly in high-altitude lakes.
Results and discussion
21
Variations in microbial community structure across and within lakes
18 15 12 2200
2400
2800 2600 Elevation (m)
3000
3200
Fig. 1. A. Map of sampled lakes on 10 m resolution elevation data of Yosemite National Park from the United States Geological Survey National Elevation Dataset (http://nationalmap.gov/). B. Lake elevation plotted against lake longitude. C. Lake temperature plotted against lake elevation for lakes sampled in July (white data points) and in August/September (black data points). In addition to temperature, multiple other environmental factors are expected to vary with elevation.
include temperature, UV radiation, atmospheric deposition of nutrients and primary production. However, several studies have examined elevational patterns in microbial diversity and community structure with mixed results: some detect significant trends (Bryant et al., 2008; Wang et al., 2012), while others do not (Fierer et al., 2011).
High-altitude lakes were frequently dominated by freshwater bacteria observed in previous studies, although the relative proportions of these groups varied across lakes and over time within individual lakes. Six bacterial phyla made up the vast majority of >2 million total 16S rRNA sequences: Proteobacteria (>730 000 sequences), Actinobacteria (>715 000 sequences), Bacteroidetes (>324 600 sequences), Verrucomibcrobia (>176 000 sequences), Cyanobacteria (>55 800 sequences) and Planctomycetes (>15 800 sequences) (Fig. 2). The remaining phyla made up
