The role of fungi in heterogeneous sediment microbial networks

Abstract

While prokaryote community diversity and function have been extensively studied in soils and sediments, the functional role of fungi, despite their huge diversity, is widely unexplored. Several studies have, nonetheless, revealed the importance of fungi in provisioning services to prokaryote communities. Here, we hypothesise that the fungal community plays a key role in coordinating entire microbial communities by controlling the structure of functional networks in sediment. We selected a sediment environment with high niche diversity due to prevalent macrofaunal bioturbation, namely intertidal mangrove sediment, and explored the assembly of bacteria, archaea and fungi in different sediment niches, which we characterised by biogeochemical analysis, around the burrow of a herbivorous crab. We detected a high level of heterogeneity in sediment biogeochemical conditions, and diverse niches harboured distinct communities of bacteria, fungi and archaea. Saprotrophic fungi were a pivotal component of microbial networks throughout and we invariably found fungi to act as keystone species in all the examined niches and possibly acting synergistically with other environmental variables to determine the overall microbial community structure. In consideration of the importance of microbial-based nutrient cycling on overall sediment ecosystem functioning, we underline that the fungal microbiome and its role in the functional interactome cannot be overlooked.

Compartmentalization of bacterial and fungal microbiomes in the gut of adult honeybees

“…Moreover, considering the cell size (e.g., in Fig. 1e–h ), fungal cells may model the spatial interactions and metabolic flow within the gut microbial community by designing the architecture of the gut and influencing the geometry of interactions among bacterial components—bacteria might exploit the surfaces made available by fungal cells to establish ecological interactions among them 67 , 85 .…”

“…Illumina libraries were prepared using the Illumina ® Nextera XT Sample Prep Kit and amplifying the V3 and V4 variable regions of the 16S rRNA gene (341F and 785R primers 115 ) from both DNA and cDNA as well as the internal transcribed spacer 2 (ITS2) region (ITS3F and ITS4R primers 85 ) from DNA, following the protocol described in Marasco et al 115 . All primers used contained an adapter for the sequencing platform and an 8-nucleotide barcode.…”

Kaustia mangrovi gen. nov., sp. nov. isolated from Red Sea mangrove sediments belongs to the recently proposed Parvibaculaceae family within the order Rhizobiales

“…Mangrove forests are highly productive ecosystems and are widespread in tropical and subtropical coastlines, with a coverage of 60–70 % [6–9]. Mangroves represent unique ecological niches as they host a diverse variety of microorganisms [10–12]. It has been estimated that the bacteria in mangrove sediments constitute up to 80 % of the total living biomass of these ecosystems [13–16] and play a key role in their functioning [12].…”

“…It has been estimated that the bacteria in mangrove sediments constitute up to 80 % of the total living biomass of these ecosystems [13–16] and play a key role in their functioning [12]. However, relatively few studies have focused on the exploration and characterization of the microbial diversity of mangrove sediments [7, 10, 11, 13, 14, 17–27] and the cultivable fraction of microbes therein [28–34]. The cultivable bacterial strains obtained from mangrove sediments include members of well-characterized genera, such as Bacillus , Halobacillus , Microbacterium , Novosphingobium , Paracoccus , Streptomyces , Thalassotalea and Vibrio [30, 33, 35–39], and several novel genera, including Acidimangrovimonas , Mangroviflexus , Mangrovibacterium , Marisediminitalea , Mangrovicoccus , Mangrovitalea , Mangrovimonas and Zhengella [32, 34, 40–45]; these data clearly confirm the untapped diversity harboured by mangrove sediments.…”

Diversity and Oil Degradation Potential of Culturable Microbes Isolated from Chronically Contaminated Soils in Trinidad

“…Fungi are particularly good candidates for remediation because (i) they have longrange transportation systems-the movement of hyphae is not limited by a hydrophobic environment, surpassing air-water interfaces and air-filled pores in soil, where they aid in the transport of extrahyphal bacteria that would otherwise be limited by this physical barrier, (ii) fungal hyphae can function in anoxic conditions, which is often the case with thick oil slicks, (iii) they can tolerate extreme environments-numerous fungi are xero-and osmotolerant and can survive in a pH range of 1 to 9 and at temperatures of 5 to 60 • C, (iv) numerous fungi have extracellular enzymes that can metabolize hydrocarbons at the start of degradation, thus aiding the process, and (v) they are capable of catabolizing recalcitrant hydrocarbons, i.e., they can metabolize and mineralize high molecular weight hydrocarbons such as PAHs, unlike bacteria (because of the low bioavailability of these compounds to bacteria) [42][43][44][45]. Extracellular enzymatic transformation of recalcitrant compounds by fungi, followed by bacterial degradation of the subsequent intermediates produced through fungal action, may contribute to a combinatorial strategy for the biodegradation of PAHs [46].…”