Application of a developed high-throughput community analysis toolset to describe the spatial and temporal dynamics of aquatic mycoplankton communities

Abstract

Aquatic fungi are a highly diverse ecological group of organisms adapted to survive in a variety of aquatic habitats ranging from alpine rivers to coral reefs and from arctic lakes to deep sea sediments. Though highly abundant and diverse in many aquatic ecosystems, there are still many gaps in our knowledge and understanding about what is shaping their community structure, distribution, and dispersal patterns. In addition, little is known about their role in the biogeochemical and carbon cycles and their position in the microbial loop and food web structures. A limiting reason was the lack of an adequate toolkit for an easy and high-throughput description of aquatic fungal communities. Therefore, the aim of my dissertation was to develop missing tools such as a primer tool and a pipeline for the analysis of fungal high-throughput 18S rRNA gene sequence datasets and to test them for ecological questions involving the spatio-temporal resolution of mycoplankton communities. In Chapter I, I present a primer toolkit consisting of a comprehensive list of 18S rRNA gene sequence primer pairs of various characteristics in respect to amplicon length, total fungal coverage, specificity on fungal taxa, and prevention of co-amplification from other eukaryotic groups. This primer list can simplify the choice of the appropriate primer pair, meeting the requirements of future fungal research studies. It can also be applied in qPCR studies. As a part of this toolkit, nu-SSU-1334-5´/nu-SSU-1648-3´ (FF390/FR1), together with the use of blocking oligos, is proposed as a suitable Illumina primer pair able to improve potential amplification biases in the investigation of environmental aquatic fungal communities. In Chapter II, I examine marine mycoplankton communities and their seasonal response to a variety of biotic and abiotic factors by sampling on a weekly basis over a one year period surface water at Helgoland Roads, North Sea (Germany). The Illumina 18S rRNA gene tag-sequencing revealed a highly diverse and dynamic fungal community over the course of the study period. The abundant members of the community were able to be categorized into four distinct groups according to their seasonal frequency patterns. Furthermore, network analyses showed that fungi are connected in multiple ways with planktonic organisms such as phytoplankton and zooplankton, but also within their own communities. The majority of the detected relationships between fungi and the planktonic organisms were negative. In an ecological context, this can be interpreted either as a top-down control of fungi on phyto- and zooplankton or as a role of fungi as a food source for zooplankton, or that fungi harmful to other plankton groups are themselves controlled by antagonistic fungi. In Chapter III, I investigate the spatial community dynamics and underlying assembling processes of aquatic fungi, in a transect line from the island of Helgoland to Lauenburg on the Elbe River (Germany). The sampling region covered a region with marine, estuarine and freshwater bodies. The aquatic fungal communities were divided into three distinct groups, primarily under the influence of local environmental conditions, and to a lesser extent under the effect of spatial control. Different assemblage processes governed the three groups: variable selection in the upstream regions and undominated processes, such as ecological drift in the downstream regions and marine waters. These results offer an important framework that helps to understand the patterns of riverine mycoplankton communities and serves as a ground for future studies so that fungi, as an essential ecological group of organisms, can be incorporated into models like, usage-balance considerations of rivers.