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As interest in natural capital grows and society increasingly recognizes the value of biodiversity, we must discuss how ecosystem observations to detect changes in biodiversity can be sustained through collaboration across regions and sectors. However, there are many barriers to establishing and sustaining large-scale, fine-resolution ecosystem observations. First, comprehensive monitoring data on both biodiversity and possible anthropogenic factors are lacking. Second, some in situ ecosystem observations cannot be systematically established and maintained across locations. Third, equitable solutions across sectors and countries are needed to build a global network. Here, by examining individual cases and emerging frameworks, mainly from (but not limited to) Japan, we illustrate how ecological science relies on long-term data and how neglecting basic monitoring of our home planet further reduces our chances of overcoming the environmental crisis. We also discuss emerging techniques and opportunities, such as environmental DNA and citizen science as well as using the existing and forgotten sites of monitoring, that can help overcome some of the difficulties in establishing and sustaining ecosystem observations at a large scale with fine resolution. Overall, this paper presents a call to action for joint monitoring of biodiversity and anthropogenic factors, the systematic establishment and maintenance of in situ observations, and equitable solutions across sectors and countries to build a global network, beyond cultures, languages, and economic status. We hope that our proposed framework and the examples from Japan can serve as a starting point for further discussions and collaborations among stakeholders across multiple sectors of society. It is time to take the next step in detecting changes in socio-ecological systems, and if monitoring and observation can be made more equitable and feasible, they will play an even more important role in ensuring global sustainability for future generations. This article is part of the theme issue 'Detecting and attributing the causes of biodiversity change: needs, gaps and solutions'. [ABSTRACT FROM AUTHOR]

Alien species have invaded worldwide and altered native biodiversity and ecosystem functions. In Lake Biwa, Japan, Micrasterias hardyi—considered an endemic species in Australia—has become one of the major dominant species since 2016. To evaluate long-term and seasonal variations in M. hardyi, we analyzed 20 years of plankton samples from the northern basin of Lake Biwa. The presence of this species was first confirmed in February 2015, and increased for long periods from November 2015 (4.2 cells cm−2) to December 2016 (2.3 × 105 cells cm−2) and from September 2017 (2.0 × 102 cells cm−2) to January 2019 (5.7 × 104 cells cm−2). Particles similar to chytrid zoosporangia were observed and attached to M. hardyi cells. However, the infection rate was low (up to 22.5%), and the infection did not seem to be a major lethal factor. We estimated that M. hardyi was introduced in the early 2000s by simple linear regression of abundance. This result indicates the existence of long time lag from introduction to detection. Moreover, as the propagule pressure to nearby water systems has been high, it is highly probable that M. hardyi has spread to other lakes and ponds via Lake Biwa. [ABSTRACT FROM AUTHOR]

Kinetoplastid flagellates are generally abundant in the deep sea and recently they were even found to be dominant in the hypolimnion of a deep freshwater lake. Therefore, to understand the distribution of kinetoplastids in deep freshwater lakes, we have collected vertical samples from five lakes in Japan. The abundance of kinetoplastids was enumerated by Catalyzed Reporter Deposition-Fluorescence in situ Hybridization, and the diversity was determined by 18S amplicon sequencing using universal eukaryote and kinetoplastid-specific primers. Kinetoplastids were abundant in the deep waters of all the lakes, contributing up to 53.6% of total nanoeukaryotes. Despite this significant contribution, kinetoplastids remain undetected by amplicon sequencing using universal primers that are widely used in eukaryotic diversity studies. However, they were detected with specific primers, and the communities were characterized by both ubiquitous and lake-specific unique OTUs. Oligotyping of a ubiquitous and dominant OTU revealed the presence of lake-specific sequence types (oligotypes). Remarkably, we also detected diplonemids (a sister group of kinetoplastids and considered to be specific in the marine habitat) using kinetoplastid-specific primers, showing their presence in freshwaters. Underestimation of kinetoplastids and diplonemids using universal primers indicates that euglenozoan flagellates are overlooked in diversity studies worldwide. The present study highlighted the importance of kinetoplastids in the hypolimnion of deep lakes, thereby indicating their role in material cycling in deep waters. [ABSTRACT FROM AUTHOR]

The grazing and lysis mortalities of planktonic bacteria were estimated using the modified dilution method and respiratory quinone (RQ) analysis in mesotrophic Lake Biwa, Japan. The planktonic bacterial assemblages in the lake consisted of various RQ subgroups with different growth and mortality rates. The sum of total bacterial mortalities due to protistan grazing and viral lysis accounted for 96.6 % (range 89.0-107.2 %) of daily total bacterial production. This is the first report that successfully demonstrates a balanced relationship between bacterial production and losses using the modified dilution method in a lake. The growth rates of ubiquinone (UQ)-containing bacteria were faster than those of menaquinone-containing bacteria. Especially the dominant and fastest growing bacterial groups in the present study were the bacterial groups containing UQ-8 or UQ-10. The sum of their production and loss accounted for 60 % of carbon fluxes within the microbial loop. Thus, a large portion of the carbon cycling through the bacterial community in Lake Biwa can be explained by the carbon fluxes through dominant bacterial groups. [ABSTRACT FROM AUTHOR]

The primary goal of the 60th anniversary symposium of the Ecological Society of Japan (ESJ) was to re-examine the role of the Society. The first of five lectures, ' Development of Long- term Ecological Research in Japan,' discussed the increasingly important role of long-term and networked research studies. Ecological research in Asia faces many challenges, because Asia features natural and anthropogenic landscapes with highly diverse ecosystems. ' Developing Strategies of the Ecological Society of Japan for Worldwide Societies of Ecology with Special Reference to Strategies for Asia' emphasized the role of ESJ in promoting ecological research and outreach in Asia. Ecosystem sustainability is a key issue in both the theory and practice of ecosystem management. A framework concept of an environmental and biodiversity cycle was proposed in the session ' Linking Community and Ecosystem Dynamics' for understanding the mechanisms driving the sustainability of ecosystems. Ecosystem services are essential aspects of land use and conservation planning and management. ' Integrating Models of Ecosystem Services and Land Use Changes' reviewed recently-developed models that simulate patterns of land-use change and analyze its effects on ecosystem services and also recommended future directions for collaboration among researchers. ' Disaster Resilience and Coastal Ecology' highlighted the contributions of ecologists to evaluating the resilience of damaged coastal ecosystems and provided sound proposals to local communities and governments for rehabilitation plans. The past achievements and future directions of ESJ were discussed by the panelists and the audience in ' Past and Future of the Ecological Society of Japan.' [ABSTRACT FROM AUTHOR]

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Uncultured bacteria affiliated with the CL500-11 cluster (phylum Chloroflexi) were first reported from the oxygenated hypolimnion of Crater Lake ( USA) as a predominant bacterioplankton, although this dominance has not been reported in other environments. In this study, we showed that CL500-11 is also dominant in the oxygenated hypolimnion of Lake Biwa ( Japan) and followed its spatiotemporal succession using fluorescent in situ hybridization. CL500-11 cells were almost absent [< 1% of 4′,6-diamidino-2-phenylindole ( DAPI)-stained cells] at the beginning of the stratification period, dominated (> 10% of DAPI-stained cells; maximum = 16.5%) in the hypolimnion during the stratification period, and decreased to below the detection limit with the collapse of the thermocline. This pattern was observed over two annual cycles. A longitudinal assessment also showed that CL500-11 was the dominant bacterium in the hypolimnion over the whole lake, but was generally undetectable in the stratified epilimnion. These data suggest that CL500-11 is acclimated to the oxygenated hypolimnion and is a potentially important component of the pelagic biogeochemical cycling of the lake. A comparative analysis of 16 S r RNA gene sequences revealed that almost all CL500-11 sequences previously deposited in the database were detected from hypolimnion or holomictic water in deep oxic freshwater lakes, suggesting that the bacteria may form one of the common lineages residing in an aerobic hypolimnetic niche. [ABSTRACT FROM AUTHOR]

We examined the growth of testate amoebae preying on Microcystis whose physiological states were different in laboratory experiments and a hypertrophic pond. We prepared three experimental systems using water samples dominated by Microcystis aeruginosa: light incubation (control), dark incubation (dark), and light incubation with addition of nitrogen and phosphorus (+NP). In all the systems, the colony density of M. aeruginosa decreased slightly during incubation. Physiological activity of phytoplankton as determined by chlorophyll fluorescence was high and almost constant in the control and +NP systems, whereas it decreased in the dark system. Cell densities of testate amoebae increased in the control and +NP systems, whereas in the dark system they remained low. Thus, growth of the amoebae was low in the systems where physiological activity of Microcystis was low. In a hypertrophic pond, cell density of testate amoebae increased and remained high when M. aeruginosa predominated. Cell density of testate amoebae increased remarkably, simultaneously with the increases in M. aeruginosa colony density and phytoplankton physiological activity. We also found a significant correlation between densities of M. aeruginosa colonies and testate amoebae. We suggested that the physiological activity of Microcystis is one important factor affecting the growth of testate amoebae grazing on Microcystis. [ABSTRACT FROM AUTHOR]

The methylthiotriazine herbicide, simetryn, is commonly used in Japan, and its concentration in surface water is often high enough to affect natural phytoplankton. To estimate how the plankton community in eutrophic systems respond to short-term exposure of realistic concentrations of simetryn, we collected plankton from a eutrophic lake and exposed them to low (20 μg l) and high (100 μg l) concentrations of simetryn for 12 days in microcosm tanks (50 l). High concentrations significantly lowered total phytoplankton biomass, particularly green algal density. Consequently, the species composition was severely modified by simetryn application. However, there was no apparent impact of simetryn on microbial food-web components, bacteria, heterotrophic nanoflagellates (HNF), and ciliates. Despite the decreased abundance of algal food, the zooplankton community showed subtle changes with simetryn application. The results indicate that the direct impact of simetryn on planktonic organisms other than phytoplankton, particularly on microbial food-web components, is weak. The indirect impact of simetryn on zooplankton through the change of food quality and quantity was also small. It has been suggested that the persistence of microorganisms, alternative food for zooplankton, probably dilutes the indirect impact of simetryn on zooplankton by compensating for the loss of food phytoplankton. Consequently, the plankton community in eutrophicated systems is resistant to the herbicide at a feasible concentration for a short period of time. [ABSTRACT FROM AUTHOR]

Abstract: A ladder lottery, known as “Amidakuji” in Japan, is a common way to choose a permutation randomly. A ladder lottery corresponding to a given permutation is optimal if has the minimum number of horizontal lines among the ladder lotteries corresponding to . In this paper we show that for any two optimal ladder lotteries and of a permutation, there exists a sequence of local modifications which transforms into . We also give an algorithm to enumerate all optimal ladder lotteries of a given permutation. By setting , the algorithm enumerates all arrangements of pseudolines efficiently. By implementing the algorithm we compute the number of arrangements of pseudolines for each . [Copyright &y& Elsevier]

Various measurements of microbial productivity in streambed pebble biofilms were analyzed almost monthly for 1 year to quantify the importance of primary production as an autochthonous source of organic matter utilized to support heterotrophic bacterial production in the dynamic food web within this natural microbial habitat. Bacterial density varied from 0.3 × 108 to 1.4 × 108 cells cm−2, and chlorophyll a concentration ranged from 0.7 to 25.9 μg cm−2, with no coupled oscillation between seasonal changes in these two parameters. In bottle incubation experiments, the instantaneous bacterial growth rate of bacteria was significantly correlated with their production rate [measured by frequency of dividing cells (FDC)] as follows: ln μ = 0.138FDC − 3.003 ( n = 15, r 2 = 0.445, p < 0.001). FDC values in the pebble biofilms increased with fluctuations during the study period, ranging from 3.6% to 9.2%. Bacterial production rates largely fluctuated between 0.15 to 0.92 μg C cm−2 h−1, and its seasonal pattern was similar to that of bacterial density. Net primary production measured between May 2002 to November 2002 attained minimum level (0.5 μg C cm−2 h−1) in June and maximum level (1.9 μg C cm−2 h−1) in August. Percentages of bacterial production to net primary production ranged between 21% and 120%. Because this ratio extends both below and above 100% for these parameters, it is likely that both autochthonous and allochthonous supplies of organic matter are important for production of bacteria in the pebble biofilms that develop in rapidly flowing fresh water streams. [ABSTRACT FROM AUTHOR]

We isolated 2 virus-like agents that suppressed growth of Gymnodinium mikimotoi from coastal waters of the Uwa Sea, Japan. The agents found in the flagellate cells, named GM6 and GM7, were filterable in a 0.22-lm-pore filter with approximately 100-nm shapes. Electron microscopic observation showed the presence of virus-like particles in severely damaged G. mikimotoi cells infected by GM6. The growth-suppression activity of the agents (GM6 or GM7) was lost by heating at 50°C, with treatments of DNase and protease, and filtration through a 0.05-lm filter. Our results suggest that the agents are DNA viruses infectious to and virulent for G. mikimotoi. This is the first report of a virus-like agent specific to G. mikimotoi. [ABSTRACT FROM AUTHOR]

Seasonal changes of seston were monitored in the pearl cultivation area of Uchiumi Bay, Ehime Prefecture, Japan, where the pearl oyster Pinctada fucata martensii is cultivated. The concentrations of chlorophyll a and particulate carbon, nitrogen and phosphorus were measured and the community structure of the phytoplankton investigated. The dominant size fraction during the study period is consumed by oyster larvae, but is too small for the adult pearl oyster. Nitzschia spp. became dominant but is indigestible for the oyster, which was thus subjected to food limitation. The authors suggest monitoring the composition of seston and phytoplankton for evaluation of the food environment of the pearl oyster.

Abstract: In this study, we sought to clarify the phylogenetic and ecological relationships of anatoxin-a-producing strains of Cuspidothrix issatschenkoi (Usačev) Rajaniemi et al. and Raphidiopsis mediterranea Skuja var. grandis Hill in Japanese lakes. We isolated 60 strains from six water bodies and evaluated their ability to produce anatoxin-a and nitrogenase, and determined the sequences of the 16S–23S rDNA internal transcribed spacer region. The results consistently indicated that all R. mediterranea ver. grandis-like strains were non-heterocytous, anatoxin-a-producing C. issatschenkoi. We also evaluated the distribution of anatoxin-a-producing strains of C. issatschenkoi in 88 water bodies using primers and a probe specifically developed in this study for quantitative PCR. By this method, we detected anatoxin-a-producing strains in 16 water bodies, while by automated rRNA intergenic spacer analysis, C. issatschenkoi was detected in 24 water bodies, indicating that the toxic and non-toxic strains occur in different environments. Although C. issatschenkoi has been classified as the functional group H1, which is tolerant to low nitrogen concentrations, the anatoxin-a-producing strains were detected from water bodies with low TOC/TON because of the lack of nitrogen-fixing ability. These results suggest that different genotypes of C. issatschenkoi have different ecotypes and prefer different environments. [Copyright &y& Elsevier]

Abstract: We studied the frequency and composition of potentially toxic cyanobacteria in 30 samples from 25 Japanese lakes using automated rRNA intergenic spacer analysis (ARISA) and eight primer sets for nodularin, microcystin, cylindrospermopsin, anatoxin-a, and saxitoxin synthetase genes. Potential microcystin- and anatoxin-a-producers were detected in 25 and 7 samples, respectively. Cylindrospermopsin- or saxitoxin-producers were not detected. PCR and clone library analyses indicated that Microcystis was the sole microcystin-producing genus. Moreover, potential microcystin-producing Microcystis strains were detected in 25 of 26 samples which included Microcystis ARISA fragments, suggesting that toxic Microcystis is ubiquitous. Potential anatoxin-a-producers detected in the samples were estimated to be Cuspidothrix issatschenkoi (synonym: Aphanizomenon issatschenkoi) from clone library analyses of the anatoxin-a biosynthesis gene cluster and 16S–23S rDNA intergenic spacer region. Anatoxin-a-producing strains of C. issatschenkoi are known from two lakes in New Zealand and Germany. In contrast, C. issatschenkoi was the second most common toxic cyanobacteria in our study. This is the first report of potential anatoxin-a-producing C. issatschenkoi strains in Asia. [Copyright &y& Elsevier]

Background: Freshwater ecosystems are inhabited by members of cosmopolitan bacterioplankton lineages despite the disconnected nature of these habitats. The lineages are delineated based on > 97% 16S rRNA gene sequence similarity, but their intra-lineage microdiversity and phylogeography, which are key to understanding the eco-evolutional processes behind their ubiquity, remain unresolved. Here, we applied long-read amplicon sequencing targeting nearly full-length 16S rRNA genes and the adjacent ribosomal internal transcribed spacer sequences to reveal the intra-lineage diversities of pelagic bacterioplankton assemblages in 11 deep freshwater lakes in Japan and Europe., Results: Our single nucleotide-resolved analysis, which was validated using shotgun metagenomic sequencing, uncovered 7-101 amplicon sequence variants for each of the 11 predominant bacterial lineages and demonstrated sympatric, allopatric, and temporal microdiversities that could not be resolved through conventional approaches. Clusters of samples with similar intra-lineage population compositions were identified, which consistently supported genetic isolation between Japan and Europe. At a regional scale (up to hundreds of kilometers), dispersal between lakes was unlikely to be a limiting factor, and environmental factors or genetic drift were potential determinants of population composition. The extent of microdiversification varied among lineages, suggesting that highly diversified lineages (e.g., Iluma-A2 and acI-A1) achieve their ubiquity by containing a consortium of genotypes specific to each habitat, while less diversified lineages (e.g., CL500-11) may be ubiquitous due to a small number of widespread genotypes. The lowest extent of intra-lineage diversification was observed among the dominant hypolimnion-specific lineage (CL500-11), suggesting that their dispersal among lakes is not limited despite the hypolimnion being a more isolated habitat than the epilimnion., Conclusions: Our novel approach complemented the limited resolution of short-read amplicon sequencing and limited sensitivity of the metagenome assembly-based approach, and highlighted the complex ecological processes underlying the ubiquity of freshwater bacterioplankton lineages. To fully exploit the performance of the method, its relatively low read throughput is the major bottleneck to be overcome in the future. Video abstract.

Diplonemids are considered marine protists and have been reported among the most abundant and diverse eukaryotes in the world oceans. Recently we detected the presence of freshwater diplonemids in Japanese deep freshwater lakes. However, their distribution and abundances in freshwater ecosystems remain unknown. We assessed abundance and diversity of diplonemids from several geographically distant deep freshwater lakes of the world by amplicon-sequencing, shotgun metagenomics and catalysed reporter deposition-fluorescent in situ hybridization (CARD-FISH). We found diplonemids in all the studied lakes, albeit with low abundances and diversity. We assembled long 18S rRNA sequences from freshwater diplonemids and showed that they form a new lineage distinct from the diverse marine clades. Freshwater diplonemids are a sister-group to a marine clade, which are mainly isolates from coastal and bay areas, suggesting a recent habitat transition from marine to freshwater habitats. Images of CARD-FISH targeted freshwater diplonemids suggest they feed on bacteria. Our analyses of 18S rRNA sequences retrieved from single-cell genomes of marine diplonemids show they encode multiple rRNA copies that may be very divergent from each other, suggesting that marine diplonemid abundance and diversity both have been overestimated. These results have wider implications on assessing eukaryotic abundances in natural habitats by using amplicon-sequencing alone., (© 2020 Society for Applied Microbiology and John Wiley & Sons Ltd.)

Microcystis aeruginosa was quantitatively surveyed in 88 freshwater environments across Japan within 3‍ ‍weeks in 2011. In order to clarify the distribution pattern of M. aeruginosa at the intra-species level, three major genotypes, which were defined by 16S-23S rRNA inter-transcribed-spacer (ITS) regions, were selectively detected using quantitative real-time PCR assays. Of the 68 sites at which the Microcystis intergenic-spacer region of the phycocyanin (IGS-PC) gene was detected, the M. aeruginosa morphotype-related genotype (MG1) dominated in 41 sites, followed by the non-toxic M. wesenbergii-related genotype (MG3). A correlation analysis showed that total nitrogen and phosphate positively correlated with the abundance of IGS-PC, which positively correlated with microcystin synthetase gene abundance. A redundancy analysis of genotype compositions showed that pH positively correlated with the dominance of MG3 and negatively correlated with MG1, i.e., both toxic and non-toxic genotypes. Our survey of Microcystis populations over a wide area revealed that MG1 is a dominant genotype in Japan.

Metagenomics has dramatically expanded the known virosphere, but freshwater viral diversity and their ecological interaction with hosts remain poorly understood. Here, we conducted a metagenomic exploration of planktonic dsDNA prokaryotic viruses by sequencing both virion (<0.22 μm) and cellular (0.22-5.0 μm) fractions collected spatiotemporally from a deep freshwater lake (Lake Biwa, Japan). This simultaneously reconstructed 183 complete (i.e., circular) viral genomes and 57 bacterioplankton metagenome-assembled genomes. Analysis of metagenomic read coverage revealed vertical partitioning of the viral community analogous to the vertically stratified bacterioplankton community. The hypolimnetic community was generally stable during stratification, but occasionally shifted abruptly, presumably due to lysogenic induction. Genes involved in assimilatory sulfate reduction were encoded in 20 (10.9%) viral genomes, including those of dominant viruses, and may aid viral propagation in sulfur-limited freshwater systems. Hosts were predicted for 40 (21.9%) viral genomes, encompassing 10 phyla (or classes of Proteobacteria) including ubiquitous freshwater bacterioplankton lineages (e.g., Ca. Fonsibacter and Ca. Nitrosoarchaeum). Comparison with viral genomes derived from published metagenomes revealed viral phylogeographic connectivity in geographically isolated habitats. Notably, analogous to their hosts, actinobacterial viruses were among the most diverse, ubiquitous and abundant viral groups in freshwater systems, with potential high lytic activity in surface waters., (© 2019 Society for Applied Microbiology and John Wiley & Sons Ltd.)

The importance of analyzing the determinants of biodiversity and community composition by using multiple trophic levels is well recognized; however, relevant data are lacking. In the present study, we investigated variations in species diversity indices and community structures of the plankton taxonomic groups-zooplankton, rotifers, ciliates, and phytoplankton-under a range of local environmental factors in pond ecosystems. For each planktonic group, we estimated the species diversity index by using linear models and analyzed the community structure by using canonical correspondence analysis. We showed that the species diversity indices and community structures varied among the planktonic groups and according to local environmental factors. The observed lack of congruence among the planktonic groups may have been caused by niche competition between groups with similar trophic guilds or by weak trophic interactions. Our findings highlight the difficulty of predicting total biodiversity within a system, based upon a single taxonomic group. Thus, to conserve the biodiversity of an ecosystem, it is crucial to consider variations in species diversity indices and community structures of different taxonomic groups, under a range of local conditions.

Subsidy between ecosystems has been considered in many natural ecosystems, and should alter food webs and communities in human-impacted ones. We estimated how drifting plankton from a reservoir contribute to downstream food webs and showed that they alter community structures over a 10-km reach below the dam. To estimate the contribution of the drifting plankton to macroinvertebrates, we used C and N isotopes and an IsoSource mixing model. In spring and autumn, contributions of plankton to collector-filterer species were highest 0.2 km downstream of the dam, and clearly decreased from 0.2 to 10 km. At 0.2 km, the contribution of plankton to a predator stonefly was remarkably high. These results indicated that drifting plankton from a dam reservoir could subsidize downstream food webs and alter their energy base, but the importance of this subsidy decreased as distance from the reservoir increased. The general linear models indicated that the abundance of collector-filterers and predators was related positively to zooplankton density in stream water. Thus, food source alteration by drifting plankton also influenced the community structures downstream of the dam.

Marine birnaviruses (MABVs) infect a wide range of fish and shellfish, yet their mode of transmission is still unclear. To determine whether marine plankton serve as a vector for MABVs, we examined plankton collected from the Uwa Sea, Japan. The phytoplankton and zooplankton were collected monthly, at depths of 0 and 40 m, from May to November 2001. Detection of the MABV genome was carried out using 2-step PCR and virus isolation. Viral genome was detected in zooplankton collected at 0 m depth in September and at 40 m depth in November. The virus could not be isolated in the PCR-positive samples. These results suggest that zooplankton may act as a vector of MABVs, although the infective and/or accumulated virus titer in zooplankton was low.