diversity Article Microbiome Changes of Endemic Lake Baikal Sponges during Bleaching Syndrome Development Valeria Itskovich 1, * , Oxana Kaluzhnaya 1 , Olga Glyzina 1 , Ragothaman Prathiviraj 2 , George Seghal Kiran 3 and Joseph Selvin 2   Citation: Itskovich, V.; Kaluzhnaya, O.; Glyzina, O.; Prathiviraj, R.; Seghal Kiran, G.; Selvin, J. Microbiome Changes of Endemic Lake Baikal Sponges during Bleaching Syndrome Development. Diversity 2021, 13, 653. https://doi.org/10.3390/d13120653 Academic Editor: Michael Wink Received: 16 November 2021 Accepted: 2 December 2021 Published: 8 December 2021 Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- iations. Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). 1 Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya, 664033 Irkutsk, Russia; x-sun77@rambler.ru (O.K.); glyzina@lin.irk.ru (O.G.) 2 Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry 605014, India; raj.prathivi@gmail.com (R.P.); josephselvinss@gmail.com (J.S.) 3 Department of Food Science and Technology, School of Life Sciences, Pondicherry University, Puducherry 605014, India; seghalkiran@gmail.com * Correspondence: itskovich@mail.ru Abstract: The sponge (Porifera) microbiome is an indicator of both natural and anthropogenic stressors. Studying Baikal sponge microbial communities could help reveal if there is a connection between bacterial symbionts and a mass sponge bleaching event that was recently detected; 16S rRNA sequencing was performed among healthy and diseased freshwater sponges of Lubomirskia baikalensis and Baikalospongia intermedia, which were collected from Lake Baikal, Russia. A phylum-based taxonomic classification showed that Chlorophyta, Acidobacteria, Bacteroidetes, Actinobacteria and Cyanobacteria were most abundant across samples. When comparing healthy and diseased L. baikalensis samples, large variations in microbial composition were found at the phylum level. Comparative analyses, which were performed for the first time for B. intermedia, showed a decrease in Chlorophyta (unicellular green algae) and an increase in Bacteroidetes and Cyanobacteria in diseased specimens. At the genus level, the Opitutus (Verrucomicrobia), Planctomyces, and Nitrospira content increased in all diseased sponges, which reflected a general tendency toward an increase in Cyanobacteria in diseased sponges. Comparative analysis of the diseased and healthy sponge metagenomes showed that diseased sponges underwent various nonspecific changes in bacterial composition. The bacterial community composition is probably influenced by sponge type and degree of disease affection. Keywords: Porifera; microbiome; sponge disease; 16S rRNA sequencing; Baikal 1. Introduction Sponges (Porifera) constitute an important component of marine and freshwater ecosystems because of their species’ richness, abundance, and key functional roles [1–4]. Sponges are inhabited by a wide variety of microorganisms, including archaea, het- erotrophic bacteria, cyanobacteria, microscopic algae (green, red, cryptophytic, diatoms), di- noflagellates, and fungi; these microorganisms account for up to 50% of their biomass [5–7]. Sponge bacterial communities tend to be dominated by Gamma-, Alphaproteo-bacteria, Actinobacteria, Cyanobacteria, Chloroflexi and Poribacteria [8–10]. Sponge symbiotic communities are based on complex functional relationships that were formed during the adaptation of the entire community to environmental condi- tions [11,12]. Microorganisms can be alternative sources of energy and carbon for the sponge, take part in the nitrogen cycle, protect against oxidative stress, and produce vari- ous bioactive metabolites [9,12,13]. In aquatic ecology, metagenomic approaches make it possible to investigate complex microbial communities and their interactions with the host and with the environment. Diversity 2021, 13, 653. https://doi.org/10.3390/d13120653 https://www.mdpi.com/journal/diversity