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We tested the hypothesis that long-term brightening of solar radiation and changes in the underwater light climate would increase the primary production of phytoplankton in the springtime in Lake Kasumigaura, Japan. Global solar radiation fluctuates on a decadal scale, and the solar radiation in May has been increasing since the 1990s in Japan. We developed a model of depth-integrated primary production (gC m−2 h−1) based on long-term monitoring data. The model based on photosynthesis-irradiance curve clarified that primary production increased by 13.2%, from 0.093 gC m−2 h−1 in 1992 to 0.105 gC m−2 h−1 in 2019, because of the combined effects of solar radiation and water temperature increases. Sensitivity analysis of the model showed that primary production was most sensitive to water quality parameters, i.e. the light attenuation coefficient and nutrient effects on Pmax. Nutrient effects were significantly correlated with the particulate organic carbon to nitrogen ratio, indicating that nitrogen shortage in phytoplankton cells may affect primary production. These results suggest that long-term springtime increases in solar radiation and water temperature increase primary production, but that water quality also controls primary production.

Burrow structures produced by various benthic animals in sediments are important components of aquatic ecosystems, allowing the circulation of interstitial water via ingress of fresh bottom water into the burrows upon feeding and intraburrow migration. Although X-ray computed tomography has been used to visualize burrow structures, it could not reveal the structures in the soft mud in Lake Kasumigaura, where evaluation of the water-circulation effect of burrows is an important issue. Here, we describe the first attempt to use magnetic resonance (MR) imaging (MRI) to visualize intact burrow structures in the soft mud sediment cores collected from a eutrophic lake. Our MRI application clarified the dynamic distribution of burrows inhabited by chironomids in the soft mud that previous studies could not visualize. By examining the relationships between the degree of chloride ion depletion in deeper layers and the burrow density calculated from the MR images, we were able to consistently explain the water-circulation effect of burrows, suggesting the higher reliability of burrow density calculated from MR images. In addition, we were able to evaluate the activity of burrows, which is difficult to achieve in sediment core experiments. We observed a smaller water-circulation effect of burrows on ammonium ions than on chloride ions, suggesting the enhancement of ammonium production or release in burrow-rich sediments.

Purpose There is increased recognition of the importance of mangroves worldwide, with efforts being made to sustainably manage these ecosystems for forestry and fishery use. Although successive monitoring of mangrove growth after planting has been conducted in some afforestation stands, measurements of soil environmental changes accompanying the plant growth have not been made in most stands. In this study, we observed the interactive relationship between the growth of mangrove, Rhizophora stylosa, and soil chemical properties at an afforestation stand on Tarawa atoll, Kiribati.Methods We first estimated root biomass in the stand. Next, we measured the concentrations of dissolved phosphorus, nitrogen, and other ions (Br−, Ca2+, K+, Na+, Cl−, and SO42−) in soil pore water, as well as the isotopic ratio of leaf carbon and nitrogen in patches of different plant ages. Results Differences in salt stress among the patches were reflected in leaf δ13C, suggesting it would be a good indicator of the physiological response of mangrove plants to salinity. Estimated root biomass was positively related with phosphate and nitrate concentrations in soil pore water, indicating the formation of a rhizosphere environment with the occurrence of root–microorganism interactions. Leaf δ15N analysis suggested that the discrimination of nitrogen isotopes during nitrification and/or uptake of NH4+ and NO3− occurs in accordance with plant growth. Conclusions Our findings revealed the changes that occur in the chemical properties of mangrove leaves and soil pore water after mangrove plantation on a yearly basis, which can improve our understanding of environmental succession during the formation of mangrove ecosystems.

Nitrogen-fixing activity has been observed in the rhizosphere of mangrove ecosystems, suggesting a close mangrove–diazotroph relationship. In regularly flooded soil, however, the pathway by which atmospheric nitrogen reaches the diazotrophs in the rhizosphere is unknown. This study provides evidence that mangrove aerial roots serve as pathways that supply nitrogen gas to the diazotrophs colonizing buried roots. A plastic chamber was attached on the exposed part of a Rhizophora stylosa Griff prop root, and 15N2 tracer gas was injected into it. The entire root, including the below-ground part, was collected for analysis of 15N labelling and nitrogenase activity. We detected 15N labelling in buried root materials 2 h after gas injection. Compared with the δ15N contents in root material from an untreated tree, the increment was >10‰ in lateral roots. The nitrogenase activity measured on the other R. stylosa roots was highest in lateral roots, matching well with the results of 15N labelling. Our results indicate that atmospheric nitrogen is taken into aerial mangrove roots through lenticels, diffuses into the buried root system and is fixed by diazotrophs. The unusual appearance of mangrove aerial roots, which has intrigued researchers for many years, could be a key to the high productivity of mangrove ecosystems.

Although long-term ecosystem monitoring provides essential knowledge for practicing ecosystem management, analyses of the causal effects of ecological impacts from large-scale observational data are still in an early stage of development. We used causal impact analysis (CIA)-a synthetic control method that enables estimation of causal impacts from unrepeated, long-term observational data-to evaluate the causal impacts of extreme water-level drawdowns during summer on subsequent water quality. We used more than 100 years of transparency and water level monitoring data from Lake Biwa, Japan. The results of the CIA showed that the most extreme drawdown in recorded history, which occurred in 1994, had a significant positive effect on transparency (a maximum increase of 1.75 m on average over the following year) in the north basin of the lake. The extreme drawdown in 1939 was also shown to be a trigger for an increase in transparency in the north basin, whereas that in 1984 had no significant effects on transparency. In the south basin, contrary to the pattern in the north basin, the extreme drawdown had a significant negative effect on transparency shortly after the extreme drawdown. These different impacts of the extreme drawdowns were considered to be affected by the timing and magnitude of the extreme drawdowns and the depths of the basins. Our approach of inferring the causal impacts of past events on ecosystems will be helpful in implementing water-level management for ecosystem management and improving water quality in lakes.

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. Supplementary Information The online version contains supplementary material available at 10.1186/s40168-020-00974-y.

The natural abundance of stable isotopes is a powerful tool for evaluating biological reactions and process conditions. However, there are few stable isotope studies on the wastewater treatment process. This study carried out the first investigation on variations in natural abundance of carbon and nitrogen stable isotope ratios (δ13C and δ15N) of activated sludge in four types of advanced treatment process (extended aeration activated sludge (EAAS), aerobic-anoxic-aerobic (A2O), recycled nitrification-denitrification (RND), and modified Bardenpho (MB)) at a municipal wastewater treatment plant. The δ13C and δ15N values of influent suspended solids settled in the primary sedimentation tank (i.e., primary sludge) ranged from -25.4‰ to -24.6‰ and 0.5‰-2.9‰, respectively, during monitoring periods. The δ13C values of the activated sludge were -24.6‰ to -23.6‰ (EAAS), -25.4‰ to -24.3‰ (A2O), -25.7‰ to -24.9‰ (RND), and -25.7‰ to -24.3‰ (MB). The δ13C values of the activated sludge were similar to those of influent suspended solids. However, the δ13C values of activated sludge in EAAS was significantly higher than in A2O, RND, and MB. Meanwhile, the δ15N values of activated sludge were obviously higher than influent suspended solids; 5.8‰-7.5‰ (EAAS), 6.6‰-8.1‰ (A2O), 5.5‰-7.5‰ (RND), and 5.3‰-7.6‰ (MB). Changes in δ13C and δ15N values of the activated sludge within the treatment system were also found. These findings indicate that changes in δ13C and δ15N values of the activated sludge rely on important function for biological wastewater treatment such as nitrification, denitrification, and methane oxidation through wastewater treatment over time.

Bacterial production has been often estimated from DNA synthesis rates by using tritium-labeled thymidine. Some bacteria species cannot incorporate extracellular thymidine into their DNA, suggesting their biomass production might be overlooked when using the conventional method. In the present study, to evaluate appropriateness of deoxyribonucleosides for evaluating bacterial production of natural bacterial communities from the viewpoint of DNA synthesis, incorporation rates of four deoxyribonucleosides (thymidine, deoxyadenosine, deoxyguanosine and deoxycytidine) labeled by nitrogen stable isotope (15N) into bacterial DNA were examined in both ocean (Sagami Bay) and freshwater (Lake Kasumigaura) ecosystems in July 2015 and January 2016. In most stations in Sagami Bay and Lake Kasumigaura, we found that incorporation rates of deoxyguanosine were the highest among those of the four deoxyribonucleosides, and the incorporation rate of deoxyguanosine was approximately 2.5 times higher than that of thymidine. Whereas, incorporation rates of deoxyadenosine and deoxycytidine were 0.9 and 0.2 times higher than that of thymidine. These results clearly suggest that the numbers of bacterial species which can incorporate exogenous deoxyguanosine into their DNA are relatively greater as compared to the other deoxyribonucleosides, and measurement of bacterial production using deoxyguanosine more likely reflects larger numbers of bacterial species productions.

To explore the mechanisms in the deposition and release of phosphorus (P) in the sediment of a shallow eutrophic lake using preserved samples, we investigated the vertical and temporal changes in P, manganese (Mn), sulfur (S), iron (Fe), aluminum (Al), calcium (Ca), and magnesium (Mg) in the sediment samples and the phosphate in the sediment pore water samples over a period of 6 years. The upper 15 cm of sediment from Lake Kasumigaura in Japan was collected monthly from 2003 to 2008 from the center of the lake. Sediment cores were divided into seven depth segments and were acid-digested for an elemental analysis via inductively coupled plasma atomic emission spectroscopy. Phosphate concentrations of the sediment pore water were determined using the molybdenum blue method. A multiple regression analysis was conducted by setting the P content as the response variable and Mn, S, Fe, Al, Ca, and Mg as explanatory variables. The results of the multiple regression analysis demonstrated that P co-precipitates with Fe and Al oxides and accumulates on the sediment surface. The vertical distributions of Mn and S suggest that Mn reduction occurs within the 0–1-cm-depth layer of the sediment and that iron sulfide is actively formed in the 6–10-cm-depth layer of the sediment. These findings imply that the layer in which ferric oxides are reduced to ferrous ions is present near the 1–6-cm-depth layer of the sediment. This layer corresponds to the layer in which the maximum phosphate concentration of the sediment pore water often occurred (the 2–6-cm-depth layer). These results indicate that vertical distributions of mineral elements are useful for assessing P dynamics in sediments. The lake sediments record the dynamics of P in the sediment. Our analytical approach using long-term observation data demonstrated that the accumulation and release of P associated with a change in the redox state can be assessed based on the vertical distributions of mineral elements in the lake sediments.

Freshwater bacterioplankton in the oxygenated hypolimnion are reportedly dominated by specific members that are distinct from those in the epilimnion. However, no consensus exists regarding the ubiquity and abundance of these bacterioplankton, which is necessary to evaluate their ecological importance. The present study investigated the bacterioplankton community in the oxygenated hypolimnia of 10 deep freshwater lakes. Despite the broad geochemical characteristics of the lakes, 16S rRNA gene sequencing demonstrated that many predominant lineages in the hypolimnion were shared by several lakes and consisted of members occurring in the entire water layer and members specific to the hypolimnion. Catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) revealed that representative hypolimnion-specific lineages, CL500–11 (Chloroflexi), CL500–3, CL500–37, CL500–15 (Planctomycetes), and the MGI group (Thaumarchaeota), together accounted for 1.5–32.9% of all bacterioplankton in the hypolimnion of the lakes. Furthermore, an analysis of micro-diversification based on single-nucleotide variation in the partial 16S rRNA gene sequence (oligotyping) suggested the presence of hypolimnion-specific ecotypes among the lineages occurring in the entire water layer (e.g., acI and Limnohabitans). Collectively, these results demonstrate the uniqueness, ubiquity, and quantitative significance of bacterioplankton in the oxygenated hypolimnion, motivating future studies to focus on their eco-physiological characteristics.

Agriculture faces the great challenge of developing strategies to maintain production while simultaneously reducing environmental impacts. The trade‐off between crop production and water quality services is one of the most serious issues facing agriculture, and interest in achieving win–win outcomes through management of ecosystem services is growing. Although wetlands can reduce nitrogen loads, it is unclear whether maintaining and restoring wetlands can ameliorate the trade‐off between crop production and water quality and thereby increase the likelihood of win–win outcomes. We defined the orthogonal residuals from the regression line relating the trade‐offs between two conflicting services as the degree to which the trade‐off was mitigated (mitigation effectiveness score). The more positive the residual, the higher mitigation effectiveness score, and the greater the potential to mitigate the trade‐off. We measured nitrate concentrations, as an indicator of water quality, five times during summer and winter across 49 sub‐watersheds of the watershed of Lake Kasumigaura, which is highly nitrogen‐loaded by agriculture. We quantified the mitigation effectiveness score from the trade‐off relationships between cropland area and nitrate concentrations, and we also identified landscape and environmental factors that affected these scores. Some sub‐watersheds in our study had high cropland cover but low nitrate concentrations. Overall, we found that mitigation effectiveness scores were positively associated with wetland cover at all sampling times. Other factors, including covers of paddy rice fields, abandoned rice fields, and impervious surfaces, and dissolved organic carbon concentrations, had no significant effects on mitigation effectiveness scores, although these factors were considered to increase nitrogen removal. Our findings suggest that maintaining and restoring wetlands might mitigate the trade‐off between crop production and water quality and thereby enhance the likelihood of win–win outcomes in agricultural landscapes. Because wetland area has decreased, flooding or ponding abandoned rice fields may be an important alternative management option. The nitrate concentrations we observed met the water quality standard for drinking water, but the fact that they sometimes exceeded the nitrogen environmental target adopted within Lake Kasumigaura in terms of eutrophication suggests that simultaneous reduction of croplands and fertilizer inputs should still be encouraged.