Microbial ecology of four coral atolls in the Northern Line Islands

Abstract

Microbes are key players in both healthy and degraded coral reefs. A combination of metagenomics, microscopy, culturing, and water chemistry were used to characterize microbial communities on four coral atolls in the Northern Line Islands, central Pacific. Kingman, a small uninhabited atoll which lies most northerly in the chain, had microbial and water chemistry characteristic of an open ocean ecosystem. On this atoll the microbial community was equally divided between autotrophs (mostly Prochlorococcus spp.) and heterotrophs. In contrast, Kiritimati, a large and populated ( approximately 5500 people) atoll, which is most southerly in the chain, had microbial and water chemistry characteristic of a near-shore environment. On Kiritimati, there were 10 times more microbial cells and virus-like particles in the water column and these microbes were dominated by heterotrophs, including a large percentage of potential pathogens. Culturable Vibrios were common only on Kiritimati. The benthic community on Kiritimati had the highest prevalence of coral disease and lowest coral cover. The middle atolls, Palmyra and Tabuaeran, had intermediate densities of microbes and viruses and higher percentages of autotrophic microbes than either Kingman or Kiritimati. The differences in microbial communities across atolls could reflect variation in 1) oceaonographic and/or hydrographic conditions or 2) human impacts associated with land-use and fishing. The fact that historically Kingman and Kiritimati did not differ strongly in their fish or benthic communities (both had large numbers of sharks and high coral cover) suggest an anthropogenic component in the differences in the microbial communities. Kingman is one of the world's most pristine coral reefs, and this dataset should serve as a baseline for future studies of coral reef microbes. Obtaining the microbial data set, from atolls is particularly important given the association of microbes in the ongoing degradation of coral reef ecosystems worldwide.

Figure 1. Maps of the sites surveyed on the four Northern Line Island atolls.

The locations for the water chemistry, microbe/viral direct counts, and Vibrio spp. culturing are indicated with the first letter of the atoll name (X for Kiritimati sites) and sequentially numbered. The sites for the metagenomes are labeled with an *. Coral cover, fish counts, and other macro-organism data were sampled at all of these sites, as well as additional sites . The prevailing current is shown as a grey arrow. MIC = number of microbes per ml; Vibr = number of culturable Vibrio spp. on TCBS plates per ml; DOC = dissolved organic carbon in µM; TDIN = total dissolved inorganic nitrogen in µM (nitrite and nitrate, and ammonium). Maps were taken from Google Earth.

Figure 2. Direct counts were used to determine the mean abundance (±standard error) of A) microbial cells (Bacteria and Archaea), B) virus-like particles (VLPs), and C) protists on the four Northern Line Island atolls.

Figure 3. Taxonomic and metabolic potential of Bacteria and Archaea of the four atolls: A) Proportion of autotrophs, heterotrophs and potential pathogens identified by the 16S rDNA sequences in the microbial metagenomic fractions.

B) Number of cultured Vibrio spp. (bar represents means±standard error) in the water column (F_3,58 = 5.697, P = 0.002, Wilcoxon one-sided paired t-test showed significant differences for all atoll pairings at P = 0.05) and coral mucus (F_3,42 = 3.514, P = 0.023, Wilcoxon one-sided paired t-test showed significant differences for all atoll pairings at P = 0.05, except between Kingman and Palmyra P = 0.299). C) The metabolic potential expressed by the seven most abundant subsystems, across the atolls. These subsystems varied significantly between Kingman and Kiritimati using both XIPE and G-test (Supplementary data). Subsystems that are more closely associated with autotrophs are shown in green. The “potential pathogen” designation are known human pathogenic genera like Staphylococcus, Vibrio, and Escherichia, fish pathogens like Aeromona, and plant pathogens from the Xylella genera.

Figure 4. Analysis of the viral metagenomes showing: A) The relative abundances of phage host range by guild.

This was the product of the mean number of virus-like particles and the proportion of sequences within the small metagenomic fraction that were similar to autotrophic, heterotrophic or potential pathogenic phage hosts. B) Sequence recruitment across the Escherichia coli Φ CP4-6 prophage (which is found in highly virulent E. coli) and Prochlorococcus marinus SSMP4 (which infects an open water autotrophic cyanobacteria).

Figure 5. Relationships recorded between microbes and virus-like particle numbers on the Northern Line Islands.

Kingman (dotted line) r² = 0.807, P<0.0001; Palmyra r² = 0.039, P = 0.414; Tabuaeran (dashed line) r² = 0.324, P = 0.006; Kiritimati (solid line) r² = 0.706, P<0.0001.

Figure 6. Prevalence of unhealthy scleractinian corals compared with scleractinian coral cover.

The prevalence of unhealthy corals was negatively related to host density on both Tabuaeran (r² = 0.477, P = 0.002) and Kiritimati (r² = 0.664, P = 0.003). No relationship was found on Palmyra (r² = 0.261, P = 0.141) or Kingman (r² = 0.251, P = 0.300).

Figure 7. Water chemistry measured for the four Northern Line Island atolls.

Concentrations of A) Dissolved organic carbon (DOC), B) Total dissolved inorganic nitrogen (TDIN: nitrite and nitrate, and ammonium), and C) Dissolved inorganic phosphate are presented as means (±standard errors). D) Microbial respiration rates as determined by adding the same microbial communities to samples of seawater collected from the four atolls.

Figure 8. Seascape and photoquadrat photographs obtained from the metagenomic sampling site on Kiritimati.

White circles indicate diseased, bleached, or recently dead corals.