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Two species of the green algae Volvox sect. Volvox from the Japanese ancient lake, Lake Biwa
The green algae Volvox sect. Volvox from the Japanese ancient lake
https://orcid.org/0000-0002-9308-4498
Nozaki Hisayoshi Conceptualization Data curation Formal analysis Funding acquisition Investigation Methodology Project administration Supervision Visualization Writing – original draft Writing – review & editing 1 2 3 *
https://orcid.org/0000-0002-8989-5933
Matsuzaki Ryo Data curation Formal analysis Investigation Methodology Visualization Writing – original draft Writing – review & editing 4
Shimotori Koichi Funding acquisition Investigation Methodology Resources Supervision Writing – original draft Writing – review & editing 5
https://orcid.org/0000-0001-5796-1687
Ueki Noriko Conceptualization Funding acquisition Investigation Resources Writing – original draft Writing – review & editing 6
Heman Wirawan Conceptualization Methodology Resources Writing – review & editing 7
Mahakham Wuttipong Methodology Project administration Resources Supervision Writing – review & editing 8
https://orcid.org/0000-0001-5269-1614
Yamaguchi Haruyo Conceptualization Investigation Project administration Resources Supervision Writing – original draft Writing – review & editing 2 5
Tanabe Yuuhiko Project administration Resources Supervision Writing – original draft Writing – review & editing 2
Kawachi Masanobu Investigation Project administration Resources Supervision Writing – review & editing 2
1 Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
2 Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
3 Department of Chemical and Biological Sciences, Faculty of Science, Japan Women’s University, Tokyo, Japan
4 Faculty of Engineering, Osaka Institute of Technology, Osaka, Japan
5 Lake Biwa Branch Office, National Institute for Environmental Studies, Otsu, Shiga, Japan
6 Science Research Center, Hosei University, Tokyo, Japan
7 Department of Science and Mathematics, Faculty of Science and Health Technology, Kalasin University, Kalasin, Thailand
8 Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
Sarwar Abul Khayer Mohammad Golam Editor
Bangladesh Agricultural University, BANGLADESH
Competing Interests: The authors have declared that no competing interests exist.

* E-mail: hisayoshi.nozaki@gmail.com
23 9 2024
2024
19 9 e03105496 6 2024
2 9 2024
© 2024 Nozaki et al
2024
Nozaki et al
https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Volvox sect. Volvox is a group of green algae with unique morphological features (thick cytoplasmic bridges between somatic cells and spiny zygote walls) and a worldwide distribution. Despite research interest in the diversity of organisms in ancient lakes, Volvox sect. Volvox from ancient lakes worldwide has not been identified to the species level. Here, we established clonal cultures of two species of this group originating from Lake Biwa, an ancient lake in Japan, and performed identification based on morphological and molecular data. One was identified as Volvox kirkiorum based on the nuclear ribosomal DNA internal spacer region (ITS) sequence, bisexual (monoicous or monoecious) spheroids, and zygote morphology. The other showed genetic separation from related species based on the secondary structure of the ITS and results of phylogenetic analysis of a combined data set from the nuclear actin gene, ITS, and two plastid genes (large subunit of RuBisCO and photosystem II CP43 apoprotein gene); it represented a new phylogenetic lineage within Volvox sect. Volvox, suggesting possible endemism in Lake Biwa. This species produced bisexual spheroids with different zygote morphology and zygote number from other species with bisexual spheroids in Volvox sect. Volvox. Therefore, Volvox biwakoensis Nozaki et H. Yamaguchi sp. nov. is described herein. This is the first endemic species of the genus Volvox described from an ancient lake.

JSPS KAKENHI 19K22446, 24K08946 https://orcid.org/0000-0002-9308-4498
Nozaki Hisayoshi JSPS KAKENHI 21K06295 https://orcid.org/0000-0001-5796-1687
Ueki Noriko The Collaborative Research Fund from Shiga Prefecture entitled “Study on water quality and lake-bottom environment for protection of the soundness of water environment” under the Japanese Grant for Regional Revitalization OS2024RR1 Shimotori Koichi Network Joint Research Center for Materials and Devices 20211204, 20221238, 20231201, 20241233 https://orcid.org/0000-0001-5796-1687
Ueki Noriko This study was partially supported by a Grants-in-Aid for Scientific Research (grant numbers 19K22446 and 24K08946 for HN, 21K06295 to NU) from the Ministry of Education, Culture, Sports, Science and Technology (MEXT)/Japan Society for the Promotion of Science (JSPS) KAKENHI (https://www.jsps.go.jp/english/e-grants/), the Collaborative Research Fund (grant number OS2024RR1 to KS) from Shiga Prefecture entitled “Study on water quality and lake-bottom environment for protection of the soundness of water environment” under the Japanese Grant for Regional Revitalization (https://www.mlit.go.jp/en/index.html), and the Research Program of "Dynamic Alliance for Open Innovation Bridging Human, Environment and Materials" (grand numbers 20211204, 20221238, 20231201 and 20241233 for NU) in "Network Joint Research Center for Materials and Devices" (https://alliance.tagen.tohoku.ac.jp/english/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Data AvailabilityNew sequence data of Volvox biwakoensis, V. kirkiorum and V. sp. Sagami are available under the DDBJ/ENA/GenBank accession numbers (LCLC817957–LC817993 and LC818981). All other relevant data are within the paper and its Supporting information files.
Data Availability

New sequence data of Volvox biwakoensis, V. kirkiorum and V. sp. Sagami are available under the DDBJ/ENA/GenBank accession numbers (LCLC817957–LC817993 and LC818981). All other relevant data are within the paper and its Supporting information files.
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pmcIntroduction

Ancient lakes are the oldest lakes in the world, dating from more than 1 million ago, and they have fascinated biologists with their high endemicity and diversity of animals, land plants, and algae [1–4]. Lake Biwa is an ancient lake that is one of the largest lakes in Japan. Aquatic land plants and aquatic multicellular animals in this lake have been studied extensively, and more than 60 endemic species and infraspecific taxa are known [5]. However, the volvocine green algae from Lake Biwa have been identified based only on light microscopic features of vegetative (asexual) stages [6], with the exception of our recent study of two species of Volvox, Volvox africanus and Volvox reticuliferus [7]. Although V. reticuliferus was described as a new species, it corresponds to the subdivision of V. africanus previously recorded worldwide [7, 8] and does not represent a new lineage or endemic species.

Volvox is a typical genus of volvocine green algae with multicellular spheroids, which is comprised of approximately 22 species worldwide [7, 9]. The genus is subdivided into four sections based on differences in vegetative and zygote morphology and phylogeny [7]. Volvox sect. Volvox is a unique group characterized by the presence of thick cytoplasmic bridges between the cells of the spheroids and spiny zygote walls [7]. Approximately 11 species have been described in this section worldwide [9]. However, two species of Volvox that we collected previously from Lake Biwa (V. africanus and V. reticuliferus [7]) belong to a different section, Volvox sect. Merrillosphaera [7]. Occurrences of the genus Volvox have been recorded in Lake Tahoe, an ancient lake in California, USA; however, no species identification has been described [10, 11]. Volvox sect. Volvox has not been identified to the species level from Lake Biwa, and there are no records of Volvox sect. Volvox from other ancient lakes worldwide [9, 12].

The present study was performed to identify species of Volvox sect. Volvox originating from Lake Biwa based on morphological and molecular data from cultured material. Here, we describe the morphology, molecular phylogeny, and taxonomy of two species of this section from Lake Biwa, Volvox kirkiorum Nozaki et al. and Volvox biwakoensis Nozaki et H. Yamaguchi sp. nov. representing a new endemic lineage within this section.

Materials and methods

Ethics statement

KS collected multicellular volvocine green algae from the water column of Lake Biwa in Japan. Collection of the samples from Lake Biwa was permitted by Biodiversity Strategy Promotion Office, Department of Environment of Lake Biwa, Shiga Prefecture, Japan. NU collected water samples of Volvox from a private boat dock area connected to Sotobori (outer moat), Shinjuku-ku, Tokyo, authorized by the owner (Canal Cafe <https://www.canalcafe.jp/>).

Establishment of cultures and morphological observations

An offshore water sample was collected from Yanagasaki in the south basin (Nanko) of Lake Biwa (35.0261274, 135.8673386) on October 20, 2022. The surface area of the lake measures 670.25 km2; its average and maximum depth are 41.2 m and 103.58 m, respectively; and the elevation of the surface of the lake above sea level is 84.371 m [13]. The water temperature at this site was 20.1°C and pH was 8.0. An additional water sample was collected from the same site on October 26, 2022. Five clonal cultures of Volvox sect. Volvox (strains 2022-1021-Biwa1, 2022-1027-VVx8, 2022-1027-VVx9, 2022-1027-VVx11, and 2022-1027-VxA12) were established from these water samples using the pipette washing method [14] (Table 1). Cultures were grown in 18 × 150 mm screw-cap tubes containing 10–11 mL of artificial freshwater-6 (AF-6) medium [15] at 20°C or 25°C under a 14:10 h light:dark (L:D) cycle under cool-white fluorescent lamps with a color temperature of 5000 K at an intensity of 70–150 μmol m−2 s−1. To examine morphological details, possible bacterial contamination was removed from the cultures of 2022-1021-Biwa1, 2022-1027-VVx9, and 2022-1027-VVx11 by picking up a young spheroid still within the parental spheroid and washing several times with fresh medium using a micropipette; the young spheroid was then transferred to 10–11 mL of urea soil Volvox thiamin (USVT)/3 medium [16] or Volvox thiamin acetate (VTAC) medium [15]. Asexual spheroids were observed in actively growing cultures with 10–11 mL or 30 mL of USVT/3 medium in screw-cap tubes or Petri dishes (20 × 90 mm), respectively, at 25°C under a 14:10 h L:D cycle. To induce sexual reproduction of V. biwakoensis strain 2022-1021-Biwa1, approximately 1 mL of actively growing culture in VTAC medium was inoculated with 10–11 mL of USVT medium in a screw cap tube. This culture was grown at 25°C under a 14:10 h L:D cycle. Sexual spheroids developed within 2 weeks. In V. kirkiorum strains 2022-1027-VVx9 and 2022-1027-VVx11, sexual spheroids often developed in actively growing cultures in USVT/3 medium at 25°C. To enhance formation and maturation of zygotes, immature sexual spheroids cultured under the conditions outlined above were transferred to fresh USVT/3 or USVT medium and cultured at 25°C under a 14:10 h L:D cycle.

10.1371/journal.pone.0310549.t001 Table 1 List of species/strains used in the present phylogenetic analyses (Figs 1 and 3).

Species	Sample/strain designation	Origin of sample/strain	GenBank/EMBL/DDBJ Accession number	
ITS-1, 5.8S rDNA & ITS-2	actin	rbcL	psbC	
Volvox biwakoensis sp. nov. from Lake Biwa, Japan	2022-1021-Biwa1 (= NIES-4661) a	Water sample collected from an offshore from Yanagasaki in the south area (Lake Nanko) of Lake Biwa (35.0261274, 135.8673386) on 20 October 2022	LC817963 b	LC817974 b	LC817986 b	LC817992 b	
Volvox kirkiorum	NIES-543	Japan	AB663327	LC817972 b	AB663325	AB663326	
NIES-2740	Gifu, Japan	AB663324	LC817973 b	AB663322	AB663323	
2022-1027-VVx9 a	Water sample collected from an offshore from Yanagasaki in the south area (Lake Nanko) of Lake Biwa (35.0261274, 135.8673386) on 26 October 2022	LC817959 b	LC817970 b	LC817984 b	LC817990 b	
2022-1027-VVx11 a	LC817960 b	LC817971 b	LC817985 b	LC817991 b	
2022-1027-VVx8 a	LC817961 b				
2022-1027-VxA12 a	LC817962 b				
Volvox sp. Sagami	NIES-4021	Kanagawa, Japan	LC191308	LC818981 b	LC191316	LC191326	
NIES-4022	LC191309	LC817975 b	LC191317	LC191327	
SB01 (= NIES-4662) a	A private boat embarkation area connected to Sotobori (outer moat), Shinjuku-ku, Tokyo (35.699994, 139.742759) on 15 May, 2021	LC817964 b	LC817976 b	LC817987 b	LC817993 b	
Volvox longispiniferus	1101-NZ-5 (= NIES-4434)	Thailand	LC546057	LC817979 b	LC546062	LC546067	
Volvox barberi	UTEX 804	USA	AB663341	LC817977 b	D86835	AB044477	
Volvox capensis	NIES-3874	USA	LC034074	LC817980 b	LC033870	LC033872	
Volvox ferrisii	NIES-2736	Kanagawa, Japan	AB663336	LC817965 b	AB663334	AB663335	
Volvox globator	SAG 199.80 (= UTEX 955)	USA	AB663340	LC817981 b	D86836	AB044478	
Volvox perglobator	NIES-4259 c	USA		LC817978 b			
NIES-4258 c	MG429137		KY489662	KY489659	
Volvox rousseletii from South Africa	UTEX 1861 male	South Africa	LC817957 b	LC817967 b	LC817982 b	LC817988 b	
UTEX 1862 female	AB663342	LC817966 b	D63448	AB044479	
Volvox rousseletii from Japan	NIES-4336 female	Japan	LC493797	LC817968 b	LC493808	LC493810	
NIES-4337 male	LC817958 b	LC817969 b	LC817983 b	LC817989 b	
a Established in this study.

b Sequenced in this study.

c Treated as a single strain for phylogenetic analysis of combined data set in Fig 2.

A new clonal culture strain (SB01) of Volvox sp. Sagami (Table 1) was established from a water sample collected from a private boat dock area connected to Sotobori (outer moat), Shinjuku-ku, Tokyo (35.699994, 139.742759) on May 15, 2021. The water temperature at this site was 23.3°C with a pH of 7.5. The methods used for this species were essentially the same as described above for V. kirkiorum.

Light microscopy was performed using a BX60 microscope (Olympus, Tokyo, Japan) equipped with Nomarski optics. The spheroid cell numbers were examined as described previously [12, 17]. Individual cellular sheaths of the extracellular matrix of the spheroids were examined after mixing approximately 10 μL of cultured material with 2–5 μL of 0.002% (w/v in distilled water) methylene blue (1B-429; Waldeck GmbH & Co., Münster, Germany).

Molecular experiments

To infer the phylogenetic positions or species identity of the algae in Volvox sect. Volvox, we first determined the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA (rDNA; ITS-1, 5.8S rDNA, and ITS-2) from the five strains of Volvox sect. Volvox from Lake Biwa (Table 1, S1 Appendix) as described previously [18], and performed comparisons with those of other strains of Volvox sect. Volvox studied previously [9] (Table 1). For a more robust determination of the phylogenetic positions of the Lake Biwa species, a combined data set from the ITS, actin gene, and two plastid genes [the large subunit of RuBisCO (rbcL) gene, plus the photosystem II CP43 apoprotein (psbC) gene] were constructed from 10 species of Volvox sect. Volvox listed in Table 1. The two plastid genes were determined as described previously [18, 19]. Nucleotide sequences of a potential group I intron inserted in the Volvox sp. Sagami psbC gene were determined by direct sequencing of PCR products amplified with four primers [16]. The actin genes were determined by the method of Kimbara et al. [18] with new primers (S1 Table). The ITS sequences in the two data sets were aligned as described previously [9, 19]. The actin exon–intron sequences from 13 operational taxonomic units (OTUs) of different sequences from 19 strains of the 10 species (Table 1) were aligned using MUSCLE [20] in MEGA X [21] and included in the data matrix (3192 bp, S2 Appendix). The outgroup or root was designated based on the results of previous phylogenetic analyses [9, 19]. Bayesian inference (BI) was performed with partitioned models as described previously [9]. In addition, maximum-likelihood (ML) analyses, based on the selected models (K80+G and T92+G models for ITS and the combined data set, respectively) with 1000 bootstrap replicates [22], were performed using MEGA X. The secondary structures of ITS-2 were predicted as described previously [8, 9].

Nomenclature

The electronic version of this article in Portable Document Format (PDF) in a work with an ISSN or ISBN constitutes a published work according to the International Code of Nomenclature for algae, fungi, and plants [23]; hence, the new name contained in the electronic publication of a PLOS ONE article is effectively published under that Code from the electronic edition alone, so there is no longer any need to provide printed copies.

Results and discussion

Molecular analysis

Two different sequences were detected on examination of ITS from five strains of Volvox sect. Volvox from Lake Biwa. Strain 2022-1021-Biwa1 had a 590-bp ITS sequence (excluding the 5′ and 3′ primer sequences [17, 24]), while the other four had identical ITS sequences 558 bp in length. Based on the results of phylogenetic analysis of ITS from various OTUs of Volvox sect. Volvox [9], strain 2022-1021-Biwa1 represented a novel lineage (V. biwakoensis) (Fig 1) whereas the other four had exactly the same sequence as V. kirkiorum [19]. However, the phylogenetic relationships between V. biwakoensis and its related taxa (Volvox ferrisii, Volvox sp. Sagami, Volvox rousseletii, and V. kirkiorum) were not well resolved (Fig 1).

10.1371/journal.pone.0310549.g001 Fig 1 Molecular identification of five new strains of Volvox sect. Volvox from Lake Biwa (green), based on the Internal Transcribed Spacer (ITS) regions of nuclear ribosomal DNA (rDNA) (ITS-1, 5.8S rDNA, and ITS-2) (Table 1).

The tree was constructed based on Bayesian Inference (BI) with K80+G model. Branch lengths represent the evolutionary distances shown by the scale bar. Posterior probabilities (0.90 or more) by BI and bootstrap values (50% or more) based on 1000 replications of maximum likelihood method (with K80+G model) are described in numbers in left and right sides at branches, respectively. For alignment data, see S1 Appendix.

Phylogenetic analyses of the combined data set from the nuclear gene actin, ITS, and two plastid genes (3192 bp) showed that V. biwakoensis, V. rousseletii, V. ferrisii, and Volvox sp. Sagami formed a monophyletic group with 0.99 posterior probability (PP) on BI and 83% bootstrap support on ML analysis (Fig 2). In this monophyletic group, V. biwakoensis was sister to the clade composed of the other three species with 0.94 PP on BI and 66% bootstrap support on ML analysis (Fig 2).

10.1371/journal.pone.0310549.g002 Fig 2 Phylogenetic analysis of two species of Volvox sect. Volvox from Lake Biwa (green) based on combined data set from the Internal Transcribed Spacer (ITS) regions of nuclear ribosomal DNA (rDNA) (ITS-1, 5.8S rDNA, and ITS-2), actin gene and two chloroplast genes (rbcL and psbC) (Table 1).

The tree was constructed based on Bayesian Inference (BI) with partitioned models (rbcL: HKY+I; psbC: F81+I; ITS: K80+G, actin: K80+I). Branch lengths represent the evolutionary distances shown by the scale bar. Posterior probabilities (0.90 or more) by BI and bootstrap values (50% or more) based on 1000 replications of maximum likelihood method (with T92+G) are described by numbers in left and right sides at branches, respectively. For alignment data, see S2 Appendix.

Based on comparisons of the secondary structure of ITS-2, one or two compensatory base changes (CBCs) were found between V. biwakoensis and its sister group (V. rousseletii, V. ferrisii, and Volvox sp. Sagami) (Fig 3).

10.1371/journal.pone.0310549.g003 Fig 3 Comparison of helices of the secondary structure of nuclear ribosomal DNA internal transcribed spacer 2 transcripts between Volvox biwakoensis sp. nov. and its related species (Fig 2).

Red frames indicate compensatory base changes between V. biwakoensis and other species. Nucleotide sequence of V. rousseletii represents mixed or common bases between Japanese (JP) and African (AF) strains (Table 1).

Volvox biwakoensis sp. nov. (Fig 4)

10.1371/journal.pone.0310549.g004 Fig 4 Light microscopy of Volvox biwakoensis sp. nov. strain 2022-1021-Biwa1 from Lake Biwa.

(A–D, G–K) Bright-field microscopy. (E, F) Nomarski differential interference contrast microscopy. (A–C) Asexual spheroids with developing embryos or daughter spheroids (d). (D) Part of asexual spheroid showing individual sheaths (asterisks) and thick cytoplasmic bridges (b) between somatic cells. Stained with methylene blue. (E) Transverse section of somatic cells in asexual spheroid showing cytoplasmic bridges (b) and pyrenoid (p) in the chloroplast. (F) Side view of anterior somatic cells showing stigma (s) and pyrenoid (p) in the chloroplast. (G) Compact daughter spheroid (d) just after inversion. Note that differentiation of gonidia of the next generation is not evident. (H–K) Sexual reproduction. (H) Sexual spheroid with eggs (e) and sperm packets (sp). (I) Part of sexual spheroid showing egg (e) and sperm packet (sp). (J) Sexual spheroid with matured zygotes. (K) Matured zygotes with acute spines on zygote walls.

Asexual spheroids were ovoid with a narrow anterior face, with 4–10 (usually 5–8) developing embryos or daughter spheroids in the posterior three-fifths of the parental spheroid, and were composed of 6000–9000 cells embedded in individual sheaths at the periphery of the gelatinous matrix (Fig 4A–4D). The mature spheroid measured up to 800 μm in length. Somatic cells were biflagellate and had a cup-shaped chloroplast with a single basal pyrenoid and a single eyespot, measuring up to 8 μm in length (Fig 4E and 4F). The cells were connected by cytoplasmic bridges that were thicker than the flagella (Fig 4D–4F). The anterior somatic cells of the spheroids were ovoid to ellipsoidal with a narrow anterior face, and the cell length was greater than or nearly equivalent to the cell width (Fig 4F). In the developing embryo, reproductive cells or gonidia of the next generation were not evident until the inversion stage (Fig 4G).

Sexual spheroids were bisexual or monoicous, subspherical or ovoid in shape, measured up to 650 μm in length, and consisted of 3600–5000 somatic cells at the periphery (Fig 4H). Four to eight sperm packets and four or more (usually 7–13) eggs were distributed in the posterior two-thirds of the spheroid (Fig 4H and 4I). Mature zygotes were 9–26 in number and reddish-brown in color with a spiny cell wall (Fig 4J). Fully developed spines of the zygote wall were 5–7 μm in length, straight or slightly curved, with an acute apex (Fig 4K). Zygotes were 46–50 μm in diameter, excluding spines. Induction of zygote germination was not attempted.

Species of Volvox sect. Volvox were subdivided into two morphological types based on the differences in sexual spheroids: bisexual (monoicous) or unisexual (dioicous) [9, 12]. V. biwakoensis belonged to the bisexual type and was similar to Volvox sp. Sagami (S1 Fig) in production of less than 30 zygotes with a maximum diameter of more than 45 μm (excluding spines) (S2 Table). However, the two species could be clearly distinguished from each other by differences in length of spines on the zygote wall and phylogenetic position. The spines of V. biwakoensis are 5–7 μm in length (Fig 4), while those of Volvox sp. Sagami were short, measuring up to 3 μm in length (S2 Table and S1 Fig). In the present phylogenetic analyses based on the combined data set from four DNA regions, V. biwakoensis was sister to the large clade composed of V. rousseletii, V. ferrisii, and Volvox sp. Sagami (Fig 2) and showed CBC in the ITS-2 secondary structure from its related species (Fig 3). Therefore, V. biwakoensis is an undescribed species representing a new lineage within Volvox sect. Volvox.

Volvox kirkiorum (Fig 5)

10.1371/journal.pone.0310549.g005 Fig 5 Bright-field microscopy of Volvox kirkiorum strains 2022-1027-VVx9 (A, C, D) and 2022-1027-VVx11 (B, E-H) from Lake Biwa. (A, B) Asexual spheroids with developing embryos or daughter spheroids (d). (C, D) Part of asexual spheroids showing somatic cells. (C) Transverse section of somatic cells showing cytoplasmic bridges (b) and pyrenoid (p) in the chloroplast. (D) Side view of anterior somatic cells showing stigma (s) and pyrenoid (p) in the chloroplast. (E–H) Sexual reproduction. (E) Sexual spheroid with eggs (e) and sperm packets (sp). (F) Part of sexual spheroid showing egg (e) and sperm packet (sp). (G) Sexual spheroid with matured zygotes. (H) Matured zygotes with acute spines on zygote walls.

The strains of V. kirkiorum described here from Lake Biwa had essentially the same morphological features as the original description of this species (NIES-543, NIES-2740 [19]), especially in zygote spine morphology and zygote size, and occasional production of small sexual spheroids with up to 10 eggs and 4–8 sperm packets (S2A Fig). However, the strains from Lake Biwa sometimes produced greater numbers of zygotes in a sexual spheroid than the original description [18]. More than 90 zygotes were counted in some sexual spheroids of the Lake Biwa strain (S2B Fig), whereas the original description of V. kirkiorum indicated up 80 zygotes in a sexual spheroid [19]. However, no genetic differences were found between strains of V. kirkiorum (Table 1). Although genetic differences were detected in the actin gene sequence between strains of Volvox sp. Sagami (Fig 2), sequences of actin genes and three other DNA regions examined in the present study were identical among the four Japanese strains of V. kirkiorum, i.e., NIES-543, NIES-2740, and Lake Biwa strains 2022-1027-VVx9 and 2022-1027-VVx11 (Fig 2).

Conclusions

Based on the results of metabarcoding analysis targeting the ITS-2 rDNA regions from Lake Biwa samples [25], 10 unclassified sequences could be considered to be derived from Volvox sect. Volvox or closely related lineages (S3 Fig and S3 Appendix). These sequences were subdivided into three groups based on phylogenetic analysis in the present study. One of the three was closely related to Volvox sp. Sagami, while the second (four different sequences) formed a monophyletic group with V. kirkiorum and the third may represent an unknown basal lineage within or just outside the clade of Volvox sect. Volvox. V. kirkiorum is also distributed outside Lake Biwa in Japan (Table 1) [19]. Therefore, it may have formed a species flock within Lake Biwa and only a single genotype within this lineage may have been transmitted to other regions of Japan (Table 1) although some sequence errors may have affected the apparent genetic divergence within the lineage (S3 Fig). In contrast, ITS-2 rDNA sequences closely related to V. biwakoensis were not recognized in ITS-2 rDNA metabarcoding sequences from Lake Biwa (S3 Fig) [25]. Therefore, V. biwakoensis may be very rare in Lake Biwa. This new species exhibited genetic separation from its related species based on the ITS secondary structure (Fig 3), and the results of phylogenetic analyses of a combined data set from the nuclear gene actin, ITS, and two plastid genes showed that it represented a new phylogenetic lineage within Volvox sect. Volvox (Fig 2). Therefore, V. biwakoensis may represent possible endemism in Lake Biwa. This endemic occurrence of V. biwakoensis may reflect the geological history of Lake Biwa. Lake Biwa has a geological history of about four million years [13], while the time of divergence between V. rousseletii and V. ferrisii (Fig 2) has been estimated to be about five million years ago [26]. Since the present phylogenetic tree suggested that the V. biwakoensis lineage diverged before the divergence between V. rousseletii and V. ferrisii (Fig 2), V. biwakoensis may have been endemic to Lake Biwa from the early time of Lake Biwa. However, detailed and reliable taxonomic information on the Volvox sect. Volvox is very limited within freshwater habitats worldwide, including ancient lakes (S2 Table). Further studies, especially studies using Asian samples of Volvox sect. Volvox, are required to evaluate the endemism hypothesis of V. biwakoensis.

Taxonomic treatment

Volvox biwakoensis Nozaki & H. Yamaguchi sp. nov

Asexual spheroids ovoid with a narrow anterior face, with usually 5–8 developing embryos or daughter spheroids in the posterior three fifths of the parental spheroid, and composed of 6000–9000 cells embedded in individual sheaths of the gelatinous matrix. The mature asexual spheroid measuring up to 800 μm in length. Somatic cells having two equal flagella, a cup-shaped chloroplast with a single basal pyrenoid and a single eyespot, measuring up to 8 μm in length. Cells connected by thick cytoplasmic bridges. Anterior somatic cells ovoid to ellipsoidal with a narrow anterior face; the cell length greater than or nearly equivalent to the cell width. Reproductive cells or gonidia of the next generation not evident until the inversion stage. Sexual spheroids 3600–5000-celled, bisexual or monoicous with 4–26 eggs and 4–8 sperm packets distributed randomly within the posterior two-thirds of the spheroid, measuring up to 650 μm in length. Mature zygotes with a spiny cell wall, measuring 46–50 μm in diameter (excluding spines). Fully developed spines of zygote wall 5–7 μm in length, straight or slightly curved with an acute apex.

Holotype: Fig 4H showing eggs and sperm packets in bisexual spheroid of strain 2022-1021-Biwa1. This strain has been deposited to the Microbial Culture Collection at the National Institute for Environmental Studies, Japan [15], and available as NIES-4661. The holotype of V. biwakoensis is an effectively published illustration since it is impossible to preserve a specimen that would show the features attributed to the taxon, especially the bisexual sexual spheroid (Article 40.5 of International Code of Nomenclature for algae, fungi, and plants [23]).

Strains examined: 2022-1021-Biwa1 (= NIES-4661) (Table 1).

Etymology: The species epithet “biwakoensis” meaning “from Lake Biwa (Japanese name "Biwako")”.

Type locality: An offshore from Yanagasaki in the south basin (Nanko) of Lake Biwa, Japan (35.0261274, 135.8673386). A water samples was collected by KS on 20 October 2022.

Supporting information

S1 Table Oligonucleotide primers used for amplifying and sequencing actin genes.

(XLSX)

S2 Table Comparison of Volvox biwakoensis sp. nov. and previously described bisexual/monoicous morphological type and species of Volvox sect. Volvox.

(DOCX)

S1 Fig Bright-field microscopy of Volvox sp. Sagami strain SB01 from Tokyo, Japan.

(DOCX)

S2 Fig Bright-field microscopy of Volvox kirkiorum from Lake Biwa, Japan.

(DOCX)

S3 Fig Phylogeny of Volvox sect. Volvox and its related metabarcoding sequences (blue) based on the Internal Transcribed Spacer (ITS) regions of nuclear ribosomal DNA (rDNA) (ITS-1, 5.8S rDNA, and ITS-2).

(DOCX)

S1 Appendix Alignment used for phylogeny in Fig 1.

(TXT)

S2 Appendix Alignment used for phylogeny in Fig 2.

(TXT)

S3 Appendix Alignment used for phylogeny in S3 Fig.

(TXT)

We are grateful to staffs of MCC-NIES who helped our experimental works.

10.1371/journal.pone.0310549.r001
Decision Letter 0
Klymkowsky Michael Academic Editor
© 2024 Michael Klymkowsky
2024
Michael Klymkowsky
https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Submission Version0
9 Jul 2024

PONE-D-24-23039

Two species of the green algae Volvox sect. Volvox from the Japanese ancient lake, Lake Biwa

PLOS ONE

Dear Dr. Nozaki,

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Both reviewers call for minor revisions that expect with be simple to address. 

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Reviewer #1: Yes

Reviewer #2: Yes

**********

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Reviewer #1: Yes

Reviewer #2: N/A

**********

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Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: The manuscript "Two species of the green algae Volvox sect. Volvox from the Japanese ancient lake, Lake Biwa" by Nozaki et al. identifies two strains of Volvox sect. Volvox including a new species from Lake Biwa as an ancient lake, which is potentially an important source of ecology and biodiversity studies but lacks the taxonomic identification of Volvox sec. Volvox at the species level worldwide. Therefore the new species Volvox biwakoensis sp. nov. with distinct zygote morphology and number among the related species should shed light on the natural history of aquatic microorganisms in ancient lakes. The authors clearly and fully described the strains they established for the publication.

Major comment

In the introduction, the manuscript discusses species diversity in ancient lakes and presents the discovery of a new species in one such lake. However, the subsequent sections do not adequately address how this discovery contributes to our understanding of species diversity in ancient lakes. Does the "possible endemism" of Volvox biwakoensis (p.15 l.320) reflect the geological history of Lake Biwa?

Minor comments

p.4 ll.95-6

"the south basin (Nanko) of Lake Biwa" is appropriate because Nanko is not a separate lake from Lake Biwa.

p.12 l.257

Was germination attempted without success or it was not attempted?

p.15 l.331

"thick" instead of "chick"

Reviewer #2: I support the publication of this article after minor revision. In terms of its content and illustrations (figures and tables), the article is at a very high scientific level. I only have two critical comments.

1. It is advisable to provide additional information about the ancient Lake Biwa: the surface area of the lake, its average and maximum depth and the elevation of the surface of the lake above sea level.

2. The second critical comment concerns supporting information: in S2 Table (Comparison of Volvox biwakoensis sp. nov. and previously described bisexual/monoicous morphological type and species of Volvox sect. Volvox) the data presented on the geographical distribution of several species of Volvox are incomplete. It is necessary to add information obtained by Mary Pocock (the recognized expert in this field) about Volvox in Australia and New Zealand:

Volvox merrillii is known not only from the Philippines and India (as listed in the S2 Table), but also from Australia (New South Wales) - M.S. Cave & M.A. Pocock. Karyological Studies in the Volvocaceae. American Journal of Botany, Vol. 38, No. 10 (Dec., 1951), pp. 800-811.

Regarding the distribution of Volvox barberi and Volvox globator, it should be added that Pocock found these two species in New Zealand - Pocock M.A. Notes on the occurrence in New Zealand of Volvulina steinii Pleyfair and species of Volvox Linn. Rec. Cant. Mus., 6: 1. This hard-to-find article is cited in: Chapman VJ, Thompson RH, Segar ECM (1957) Check list of fresh-water algae of New Zealand. Trans. Roy. Soc. New Zealand. 84(4): 695–747.

**********

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Attachment Submitted filename: Review_Manuscript Number PONE-D-24-23039.docx

10.1371/journal.pone.0310549.r002
Author response to Decision Letter 0
Submission Version1
12 Jul 2024

Dear Dr. Michael Klymkowsky,

Thank you very much for your scholarly and positive decision of our manuscript entitled " Two species of the green algae Volvox sect. Volvox from the Japanese ancient lake, Lake Biwa" for publication in PLOS ONE as a research article.

Based on the comments/suggestions raised by the two reviewers, we have revised the manuscript completely. Our responses to the comments have been described in the followings:

Sincerely,

Hisayoshi Nozaki

PONE-D-24-23039

Two species of the green algae Volvox sect. Volvox from the Japanese ancient lake, Lake Biwa

PLOS ONE

When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

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Response: These three files have been uploaded. In addition, S2 Table with tracked changes and S3 Figure with tracked changes have also prepared, in addition to the unmarked revised version.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

Response: As suggested, all funding-related text has been removed from ‘Financial Disclosure’ sections of the revised manuscript. Figures 1-5 have been revised by using PACE and five tiff files of Figures 1-5 have been uploaded.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols.

We look forward to receiving your revised manuscript.

Kind regards,

Michael Klymkowsky, Ph.D.

Academic Editor

PLOS ONE

Journal Requirements:

When submitting your revision, we need you to address these additional requirements.

1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at

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Response: I have ensured that our manuscript meets PLOS ONE's style requirements, including those for file naming.

2. "We noticed you have some minor occurrence of overlapping text with the following previous publication(s), which needs to be addressed:

https://doi.org/10.1371/journal.pone.0235622

In your revision ensure you cite all your sources (including your own works), and quote or rephrase any duplicated text outside the methods section. Further consideration is dependent on these concerns being addressed."

Response: In the description of the holotype, the sentences have been changed. In addition, figure legends of Figures 1, 2, and S3 Figure have been revised in explanation of BI and bootstrap values and branch lengths. However, "Nomenclature" has not been changed because it belongs to the methods section. In S2 Table, Nozaki et al. [1] (https://doi.org/10.1371/journal.pone.0235622) was already cited in the top of the table.

3. Please note that funding information should not appear in any section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. Please remove any funding-related text from the manuscript.

Response: All funding-related text has been removed from the revised main manuscript.

4. We note that the grant information you provided in the ‘Funding Information’ and ‘Financial Disclosure’ sections do not match.

When you resubmit, please ensure that you provide the correct grant numbers for the awards you received for your study in the ‘Funding Information’ section.

Response: As described above, all funding-related text has been removed from the main manuscript of revised version.

The correct grant numbers for the awards we received for our study have been described in the ‘Funding Information’

as follows:

JSPS KAKENHI

Award Number: 19K22446, 24K08946 | Recipient: Hisayoshi Nozaki, Ph.D.

JSPS KAKENHI

Award Number: 21K06295 | Recipient: Noriko Ueki, Ph.D.

The Collaborative Research Fund from Shiga Prefecture entitled “Study on water quality and lake-bottom environment for protection of the soundness of water environment” under the Japanese Grant for Regional Revitalization

Award Number: OS2024RR1 | Recipient: Koichi Shimotori, Ph.D.

Network Joint Research Center for Materials and Devices

Award Number: 20211204, 20221238, 20231201, 20241233 | Recipient: Noriko Ueki, Ph.D.

We prepared Financial Disclosure as suggested*. However, because of the possible error of the editorial manager system of PLOS ONE, we cannot access 'Financial Disclosure' of Additional Information via the editorial manager system.

Please help me!

*This study was partially supported by a Grants-in-Aid for Scientific Research (grant numbers 19K22446 and 24K08946 for HN, 21K06295 to NU) from the Ministry of Education, Culture, Sports, Science and Technology (MEXT)/Japan Society for the Promotion of Science (JSPS) KAKENHI (https://www.jsps.go.jp/english/e-grants/), the Collaborative Research Fund (grant number OS2024RR1 to KS) from Shiga Prefecture entitled “Study on water quality and lake-bottom environment for protection of the soundness of water environment” under the Japanese Grant for Regional Revitalization (https://www.mlit.go.jp/en/index.html), and the Research Program of "Dynamic Alliance for Open Innovation Bridging Human, Environment and Materials" (grand numbers 20211204, 20221238, 20231201 and 20241233 for NU) in "Network Joint Research Center for Materials and Devices" (https://alliance.tagen.tohoku.ac.jp/english/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

5. When completing the data availability statement of the submission form, you indicated that you will make your data available on acceptance. We strongly recommend all authors decide on a data sharing plan before acceptance, as the process can be lengthy and hold up publication timelines. Please note that, though access restrictions are acceptable now, your entire data will need to be made freely accessible if your manuscript is accepted for publication. This policy applies to all data except where public deposition would breach compliance with the protocol approved by your research ethics board. If you are unable to adhere to our open data policy, please kindly revise your statement to explain your reasoning and we will seek the editor's input on an exemption. Please be assured that, once you have provided your new statement, the assessment of your exemption will not hold up the peer review process.

Response: I have asked DDBJ to release the new sequence data immediately. The DDBJ/ENA/GenBank accession numbers (LCLC817957–LC817993 and LC818981) are now available.

6. Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

Response: A book [13] has been added to reference the details of Lake Biwa (see comment 1 of Reviewer #2) and the divergence has been discussed based on the major comment by reviewer#1 by citing [26]. :

13. Kawanabe H, Nishino M, Maehata M, editors. Lake Biwa: interactions between nature and people. New York: Springer; 2012. doi: 10.1007/978-94-007-1783-1

26. Yamagishi S, Yamamoto K, Takahashi K, Kawai-Toyooka H, Suzuki S, Matsuzaki R, Yamaguchi H, Kawachi M, Higashiyama T, Nozaki H. Evolutionary analysis of MID homologs during the transition from homothallic species to heterothallic species in Volvox sect. Volvox (Chlorophyceae). Phycol. Res. 2024; 72: 46-55. doi: 10.1111/pre.12538

Additional Editor Comments:

Both reviewers call for minor revisions that expect with be simple to address.

[Note: HTML markup is below. Please do not edit.]

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: N/A

3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

4. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: The manuscript "Two species of the green algae Volvox sect. Volvox from the Japanese ancient lake, Lake Biwa" by Nozaki et al. identifies two strains of Volvox sect. Volvox including a new species from Lake Biwa as an ancient lake, which is potentially an important source of ecology and biodiversity studies but lacks the taxonomic identification of Volvox sec. Volvox at the species level worldwide. Therefore the new species Volvox biwakoensis sp. nov. with distinct zygote morphology and number among the related species should shed light on the natural history of aquatic microorganisms in ancient lakes. The authors clearly and fully described the strains they established for the publication.

Major comment

In the introduction, the manuscript discusses species diversity in ancient lakes and presents the discovery of a new species in one such lake. However, the subsequent sections do not adequately address how this discovery contributes to our understanding of species diversity in ancient lakes. Does the "possible endemism" of Volvox biwakoensis (p.15 l.320) reflect the geological history of Lake Biwa?

Response: Yes, the "possible endemism" of Volvox biwakoensis (p.15 l.320) may reflect the geological history of Lake Biwa. Thus, several sentences of discussion have been added to the conclusion section in the revised manuscript.

Minor comments

p.4 ll.95-6

"the south basin (Nanko) of Lake Biwa" is appropriate because Nanko is not a separate lake from Lake Biwa.

Response: Revised as suggested. Thank you!

p.12 l.257

Was germination attempted without success or it was not attempted?

Response: It was not attempted because of lack of abundant matured zygotes for induction of zygote germination. The description of the text has been revised: "Induction of zygote germination was not attempted."

p.15 l.331

"thick" instead of "chick"

Response: Revised as suggested. Thank you!

Reviewer #2: I support the publication of this article after minor revision. In terms of its content and illustrations (figures and tables), the article is at a very high scientific level. I only have two critical comments.

1. It is advisable to provide additional information about the ancient Lake Biwa: the surface area of the lake, its average and maximum depth and the elevation of the surface of the lake above sea level.

Response: These data have been added to the Method section of the revised manuscript.

2. The second critical comment concerns supporting information: in S2 Table (Comparison of Volvox biwakoensis sp. nov. and previously described bisexual/monoicous morphological type and species of Volvox sect. Volvox) the data presented on the geographical distribution of several species of Volvox are incomplete. It is necessary to add information obtained by Mary Pocock (the recognized expert in this field) about Volvox in Australia and New Zealand:

Volvox merrillii is known not only from the Philippines and India (as listed in the S2 Table), but also from Australia (New South Wales) - M.S. Cave & M.A. Pocock. Karyological Studies in the Volvocaceae. American Journal of Botany, Vol. 38, No. 10 (Dec., 1951), pp. 800-811.

Regarding the distribution of Volvox barberi and Volvox globator, it should be added that Pocock found these two species in New Zealand - Pocock M.A. Notes on the occurrence in New Zealand of Volvulina steinii Pleyfair and species of Volvox Linn. Rec. Cant. Mus., 6: 1. This hard-to-find article is cited in: Chapman VJ, Thompson RH, Segar ECM (1957) Check list of fresh-water algae of New Zealand. Trans. Roy. Soc. New Zealand. 84(4): 695–747.

Responses: Thank you very much for your very valuable and helpful information of distribution of Volvox sect. Volvox. These data have been described in S2Table by citing the two references, Pocock (1951), Cave & Pocock (1951).

Attachment Submitted filename: Response to Reviewers -ok2.docx

10.1371/journal.pone.0310549.r003
Decision Letter 1
Sarwar Abul Khayer Mohammad Golam Academic Editor
© 2024 Abul Khayer Mohammad Golam Sarwar
2024
Abul Khayer Mohammad Golam Sarwar
https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Submission Version1
3 Sep 2024

Two species of the green algae Volvox sect. Volvox from the Japanese ancient lake, Lake Biwa

PONE-D-24-23039R1

Dear Dr. Nozaki,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

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10.1371/journal.pone.0310549.r004
Acceptance letter
Sarwar Abul Khayer Mohammad Golam Academic Editor
© 2024 Abul Khayer Mohammad Golam Sarwar
2024
Abul Khayer Mohammad Golam Sarwar
https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
13 Sep 2024

PONE-D-24-23039R1

PLOS ONE

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