Top-down controls on bacterial community structure: microbial network analysis of bacteria, T4-like viruses and protists

Abstract

Characterizing ecological relationships between viruses, bacteria and protists in the ocean are critical to understanding ecosystem function, yet these relationships are infrequently investigated together. We evaluated these relationships through microbial association network analysis of samples collected approximately monthly from March 2008 to January 2011 in the surface ocean (0-5 m) at the San Pedro Ocean Time series station. Bacterial, T4-like myoviral and protistan communities were described by Automated Ribosomal Intergenic Spacer Analysis and terminal restriction fragment length polymorphism of the gene encoding the major capsid protein (g23) and 18S ribosomal DNA, respectively. Concurrent shifts in community structure suggested similar timing of responses to environmental and biological parameters. We linked T4-like myoviral, bacterial and protistan operational taxonomic units by local similarity correlations, which were then visualized as association networks. Network links (correlations) potentially represent synergistic and antagonistic relationships such as viral lysis, grazing, competition or other interactions. We found that virus-bacteria relationships were more cross-linked than protist-bacteria relationships, suggestive of increased taxonomic specificity in virus-bacteria relationships. We also found that 80% of bacterial-protist and 74% of bacterial-viral correlations were positive, with the latter suggesting that at monthly and seasonal timescales, viruses may be following their hosts more often than controlling host abundance.

Figure 1

Month-to-month shifts in Bray–Curtis similarity within microbial communities. (a) Average similarity within each community, observed approximately monthly, over 3 years. ‘All' indicates the average similarity of all communities (that is, bacteria, viral and protistan) combined into one meta-community. Line, average similarity; box, 25th and 75th percentiles; and error bars, 10th and 90th percentiles. (b) Bray–Curtis similarity between adjacent months for each microbial group, plotted according to the earliest month (that is, March 2008 for comparing March 2008–April 2008). (c) Correlation of bacterial abundance (y axis) and (d) shifts in bacterial Bray–Curtis similarity between adjacent months (y axis) to viral Bray–Curtis similarity (x axis).

Figure 2

Two mini networks and the relative abundance of each OTU over time. Each mini network (a and b) depicts microbial OTUs as shapes (bacteria, circles; protists, diamonds; viruses, v-shapes). Lines represent statistically significant LS correlations with LS values shown: solid lines are positive correlations and arrows are delayed correlations, pointing toward lagging OTU. Relative abundance of each node is shown as a percent of each microbial community from March 2008–December 2010 for each network (c and d). Bacterial abundance is shown by the bar graph, whereas the protistan (c) and viral (d) OTU relative abundance is indicated by the line graph. * denotes the time-shifted viral OTU, as described in Table 3.

Figure 3

Broad overview of interactions between (a) protists and bacteria only, and (b) T4-like viruses and bacteria only. Microbial nodes are bacteria, circles; protists, diamonds; viruses, v-shapes. Node color indicates its number of edges according to the scale shown in the upper right. Solid lines are positive correlations with no delay; dashed lines, negative correlations with no delay; sine-wave lines, negative-delayed correlations; and forward-slashed lines, positive-delayed correlations. Arrows point toward the lagging OTU. Note that correlations between similar taxa (for example, bacteria–bacteria, protist–protist and virus–virus) were omitted.

Figure 4

Top five bacterial OTUs differentially correlate to bacterial, viral and protistan OTUs. Top five bacterial OTUs are highlighted as white circles. All other nodes are bacteria, circles; protists, diamonds; viruses, v-shapes; abiotic, hexagon. Node labels indicate an abbreviated identity (where available) and fragment length. Note that SAR11_S1 indicates SAR11 Surface Clade 1. Solid lines are positive correlations with no delay; dashed lines, negative correlations with no delay; sine-wave lines, negative-delayed correlations; and forward-slashed lines, positive-delayed correlations. Arrows point toward the lagging OTU.

Figure 5

Cyanobacterial OTU correlations to other microbial OTUs reveal potential lytic virus–host relationships, grazing and temporal trends. Cyanobacteria OTUs are noted as white circles and labeled as Prochlorococcus (Pro) or Synechococcus (Syn), followed by ecotype designation (HL: high light; LL: low light; A/B: Synechococcus group). All other nodes are bacteria, circles; protists, diamonds; viruses, v-shapes; abiotic, hexagons. Node labels indicate an abbreviated identity (where available) and fragment length. Solid lines are positive correlations with no delay; dashed lines, negative correlations with no delay; sine-wave lines, negative-delayed correlations; and forward-slashed lines, positive-delayed correlations. Arrows point toward the lagging OTU.