Factors affecting the isolation and diversity of marine sponge-associated bacteria

Yitayal S Anteneh,Qi Yang,Christopher M M Franco,Melissa H Brown

doi:10.1007/s00253-022-11791-8

Abstract

Marine sponges are an ideal source for isolating as yet undiscovered microorganisms with some sponges having about 50% of their biomass composed of microbial symbionts. This study used a variety of approaches to investigate the culturable diversity of the sponge-associated bacterial community from samples collected from the South Australian marine environment. Twelve sponge samples were selected from two sites and their bacterial population cultivated using seven different agar media at two temperatures and three oxygen levels over 3 months. These isolates were identified using microscopic, macroscopic, and 16S rRNA gene analysis. A total of 1234 bacterial colonies were isolated which consisted of four phyla: Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes, containing 21 genera. The diversity of the bacterial population was demonstrated to be influenced by the type of isolation medium, length of the incubation period and temperature, sponge type, and oxygen level. The findings of this study showed that marine sponges of South Australia can yield considerable bacterial culturable diversity if a comprehensive isolation strategy is implemented. Two sponges, with the highest and the lowest diversity of culturable isolates, were examined using next-generation sequencing to better profile the bacterial population. A marked difference in terms of phyla and genera was observed using culture-based and culture-independent approaches. This observed variation displays the importance of utilizing both methods to reflect a more complete picture of the microbial population of marine sponges.Key pointsImproved bacterial diversity due to long incubations, 2 temperatures, and 3 oxygen levels.Isolates identified by morphology, restriction digests, and 16S rRNA gene sequencing.At least 70% of culturable genera were not revealed by NGS methods.

Highlights

Studies on biologically active metabolites are increasingly important as they can be used in multiple biotechnological applications, including as new antibiotics that are effective against multidrug-resistant pathogens
NCBI database was used for BLASTn of the sequences obtained, and the five sponge samples were identified as Sarcotragus sp. (EF646841) (RB 11), Carteriospongia foliascens (KC869574) (RB 12), Aplysilla sulfurea (EF646837) (RB 16), Dendrilla sp. (KU533858) (RB 17), and Tedania tubulifera (KJ620377) (RB 18)
A total of 1234 colony forming unit (CFU) bacteria were isolated from the many bacteria cultivated from the 12 sponge samples collected from Glenelg (310) and Rapid Bay (924)

Summary

Introduction

Studies on biologically active metabolites are increasingly important as they can be used in multiple biotechnological applications, including as new antibiotics that are effective against multidrug-resistant pathogens. Natural environments are still an important source for the discovery of novel antibiotics (Bull and Stach 2007; Claverias et al 2015). Metabolite-producing microorganisms from terrestrial environments have been investigated for many years; the chance of finding novel products from these sources is diminishing. Applied Microbiology and Biotechnology million years) (Maloof et al 2010). They are sedentary filter-feeders, able to pump thousands of liters of water each day (Bell 2008), and some have the ability to absorb dissolved organic matter (de Goeij et al 2008). Being the most dominant and diverse members of the marine community, their diversity could outnumber the combined species diversity of most organisms in the community (Van Soest et al 2012). According to the world Porifera database (Van Soest et al 2021), there are more than 9432 species of sponges spread among 680 genera and four different classes—Calcarea, Demospongiae, Hexactinellida, and Homoscleromorpha (Gazave et al 2010)

Methods

Results

Conclusion