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Bacterial Diversity in Shallow Oligotrophic Marine Benthos and Overlying Waters: Effects of Virus Infection, Containment, and Nutrient Enrichment

Abstract

Little is known of the factors shaping sediment bacterial communities, despite their high abundance and reports of high diversity. Two factors hypothesized to shape bacterial communities in the water column are nutrient (resource) availability and virus infection. The role these factors play in benthic bacterial diversity was assessed in oligotrophic carbonate–based sediments of Florida Bay (USA). Sediment–water mesocosm enclosures were made from 1-m diameter clear polycarbonate cylinders which were pushed into sediments to ˜201 cm sediment depth enclosing ˜80 L of water. Mesocosms were amended each day for 14 d with 10 µM NH +4 and 1 µM PO 3−4 . In a second experiment, viruses from a benthic flocculent layer were concentrated and added back to flocculent layer samples which were collected near the mesocosm enclosures. Photosynthesis by microalgae in virus-amended incubations was monitored by pulse-amplitude modulated (PAM) fluorescence. In both experiments, bacterial diversity was estimated using automated rRNA intergenic spacer analysis (ARISA), a high-resolution fingerprinting approach. Initial sediment bacterial operational taxonomic unit (OTU) richness (236 ± 3) was higher than in the water column (148 ± 9), where an OTU was detectable when its amplified DNA represented >0.09% of the total amplified DNA. Effects on bacterial diversity and operational taxonomic unit (OTU) richness in nutrient-amended mesocosms may have been masked by the effects of containment, which stimulated OTU richness in the water column, but depressed OTU richness and diversity in sediments. Nutrient addition significantly elevated virus abundance and the ratio of viruses to bacteria (p < 0.05 for both) in the sediments, concomitant with elevated bacterial diversity. However, water column bacterial diversity (in unamended controls) was not affected by nutrient amendments, which may be due to rapid nutrient uptake by sediment organisms or adsorption of P to carbonate sediments. Addition of live viruses to benthic flocculent layer samples increased bacterial OTU diversity and richness compared with heat-killed controls; however, cluster analyses showed that the community structure in the virus-amended mesocosms varied greatly between replicates. Despite the strong effects upon eubacterial communities, photosynthesis of co-occurring protists and cyanobacteria was not significantly altered by the presence of virus concentrates. This study supports the hypothesis that nutrient availability plays a key role in shaping sediment bacterial communities, and also that viruses may regulate the abundance of the dominant competitors and allow less dominant organisms to maintain or increase their abundance in a community due to decreased competition for resources.

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Acknowledgements

The authors thank C. Heil, D. Ault, M.B. Neely, S. Murasko (USF), G. Hitchcock, J. Jurado (UMiami, RSMAS), L. Gilbane, M.S. Schwalbach, J. Steele (USC), J. Burns (UMD), and two anonymous reviewers for helpful comments on the manuscript. We thank the entire staff and vessel operators at the FIO/FMRI Keys Marine Laboratory, Layton, Florida, for their assistance in this study. I.H. was supported by a USC Seagrant Traineeship while conducting this study. This work was supported by NSF grants OCE9906989, OCE0084231, and OCE9705523 awarded to J.A.F and NOAA/COP/SFERPM2000 Award No. NAO60PO519 to G.A.V. (G. Hitchcock, UM/RSMAS, co-PI).

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Hewson, I., Vargo, G. & Fuhrman, J. Bacterial Diversity in Shallow Oligotrophic Marine Benthos and Overlying Waters: Effects of Virus Infection, Containment, and Nutrient Enrichment . Microb Ecol 46, 322–336 (2003). https://doi.org/10.1007/s00248-002-1067-3

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Keywords

  • Bacterial Community
  • Internally Transcribe Spacer
  • Bacterial Diversity
  • Operational Taxonomic Unit
  • Terminal Restriction Fragment Length Polymorphism