Investigating local patterns in microbial communities: characterising and quantifying the links between soil and freshwater

  • Stream, Ark in Park. Image - Kiwibt

    Stream, Ark in Park. Image - Kiwibt

While studies have been conducted to investigate the biogeography of stream microbes(1, 2) and soil microbes(3, 4), there is an absence of literature connecting the two. Since there is a strong link between freshwater and terrestrial environments through hydrological networks, it seems logical that there would be a relationship between the organisms found in the soil and the stream draining the catchment. One of few studies to investigate whether stream and lake waters are indeed inoculated by soil microbes has indicated that, to an extent, bacterial communities in surface waters are indeed shaped by inoculation of microbes from the soil(5). However, the lack of replication in other streams, and unique environment in which this study was conducted make it difficult to judge whether or not these results are representative of what is happening elsewhere.


  1. Larouche JR, Bowden WB, Giordano R, Flinn MB, Crump BC. 2012. Microbial biogeography of arctic streams: exploring influences of lithology and habitat. Aquat Microbiol 3 :309.
  2. Lear G, Washington V, Neale M, Case B, Buckley H, Lewis G. 2013. The biogeography of stream bacteria. Glob Ecol Biogeogr 22 :544–554.
  3. Fierer N, Jackson RB. 2006. The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci USA 103 :626–631.
  4. Griffiths RI, Thomson BC, James P, Bell T, Bailey M, Whiteley AS. 2011. The bacterial biogeography of British soils. Environ Microbiol 13 :1642–1654.
  5. Crump BC, Amaral-Zettler LA, Kling GW. 2012. Microbial diversity in arctic freshwaters is structured by inoculation of microbes from soils. ISME J 6 :1629–1639.

By collecting both soil and stream samples within a single catchment, we want to determine whether there is a link between microbial communities in the stream and the soil microbes in the catchment.

Similar to distance decay patterns that have been observed when assessing solely soil bacteria or freshwater bacteria, we expect that the strength of the link between soil and freshwater communities will decline with increased distance of the soil sample from the stream, as soil bacterial communities closer to the stream are more likely to be inoculating the water.

The Kelly Stream catchment in the Waitakere Ranges will be used as the sampling site for this project (Fig 1).

  • Soil samples (10 cm deep, 2.5 cm wide) will be collected along each bait line; closest to the stream the samples will be collected in smaller increments (every 1 m), while moving further away, samples will be collected less frequently (up to 50 m apart), until the end of the baitline is reached.
  • Stream sampling will consist of collecting freshwater samples and sediment samples. For each freshwater sample, half a litre of freshwater will be filtered through sterile 0.22 µm nitrocellulose filters from which the DNA will later be extracted. Sediment samples will be collected from the surface of the stream bed.
  • Stream sampling will be repeated in the weeks following the initial sampling, to account for the possibility of a lag period before the soil microbes can be detected in the stream if they are indeed inoculating the water.

Figure 1: The location of the study site, and the distribution of the bait lines throughout the catchment. There are a total of 11 bait lines, and 133 bait stations.

Figure 1: The location of the study site, and the distribution of the bait lines throughout the catchment. There are a total of 11 bait lines, and 133 bait stations.