Decomposing diversity into measures of evenness, similarity, and richness.

It has long been recognized that diversity has many measurable aspects, such as richness, evenness, and similarity among species. However, given a diversity index, it is unclear whether it necessarily can be decomposed into components that reflect these different aspects. Here, we present a scheme to decompose the Leinster and Cobbold diversity index, which subsumes and generalizes many other indices, into the components of richness, evenness and taxonomic similarity. Our approach addresses the problem that in general a vector of equal relative abundances does not maximize diversity. Furthermore, our approach uses all available information to give unbiased estimates of both evenness and similarity.

High Microeukaryotic Diversity in the Cold-Seep Sediment.

Microeukaryotic diversity, community structure, and their regulating mechanisms remain largely unclear in chemosynthetic ecosystems. Here, using high-throughput sequencing data of 18S rRNA genes, we explored microeukaryotic communities from the Haima cold seep in the northern South China Sea. We compared three distinct habitats: active, less active, and non-seep regions, with vertical layers (0-25 cm) from sediment cores. The results showed that seep regions harbored more abundant and diverse parasitic microeukaryotes (e.g., Apicomplexa and Syndiniales) as indicator species, compared to nearby non-seep region. Microeukaryotic community heterogeneity was larger between habitats than within habitat, and greatly increased when considering molecular phylogeny, suggesting the local diversification in cold-seep sediments. Microeukaryotic α-diversity at cold seeps was positively increased by metazoan richness and dispersal rate of microeukaryotes, while its ß-diversity was promoted by heterogeneous selection mainly from metazoan communities (as potential hosts). Their combined effects led to the significant higher γ-diversity (i.e., total diversity in a region) at cold seeps than non-seep regions, suggesting cold-seep sediment as a hotspot for microeukaryotic diversity. Our study highlights the importance of microeukaryotic parasitism in cold-seep sediment and has implications for the roles of cold seep in maintaining and promoting marine biodiversity.

Expression and significance of serum vitamin D and LL-37 levels in infants with bacterial pneumonia.

Objective: To investigate the significance of vitamin D and human antimicrobial peptide LL-37 in the occurrence and development of bacterial pneumonia in infants. Methods: From January 2021 to January 2022, 80 infants with bacterial pneumonia were selected, including 33 cases of gram-positive bacterial infection (GP) and 47 cases of gram-negative bacterial infection (GN). During the same period, 40 infants who underwent health examination in The Affiliated Hospital of Hangzhou Normal University served as the healthy control group. On the day of admission, peripheral blood was collected from pneumonia patients, and during physical examination of controls; and serum LL-37 levels were measured by enzyme-linked immunosorbent assay (ELISA) and serum 25-hydroxyvitamin D [25(OH)D] levels were measured by electrochemiluminescence. The differences in serum LL-37 and 25(OH)D levels and their correlation with disease severity were compared. Pearson correlation was used to analyze the correlation between serum 25(OH)D and LL-37 levels in infants with bacterial pneumonia. Results: The levels of 25(OH)D and 25(OH)D deficiency were significantly lower in patients than in controls (all P < 0.05), and the levels of serum LL-37 were significantly higher in pneumonia patients than in controls (P < 0.05). There was no significant difference in serum 25(OH)D and LL-37 levels between cases with GP and GN (all P > 0.05). The serum 25(OH)D level was lower in the severe pneumonia group than in the mild pneumonia group and controls, and the 25(OH)D deficiency rate was higher; the difference was statistically significant (all P < 0.05). The LL-37 level in the severe pneumonia group was lower than that in the mild pneumonia group but higher than that in the control group, and the difference was statistically significant (P < 0.05). The 25(OH)D level was positively correlated with the LL-37 level (r = 0.8, P < 0.05), and the 25(OH)D level was negatively correlated with procalcitonin (PCT) and length of hospital stay (rs = -0.3, -0.3, P < 0.05); the LL-37 level was negatively correlated with PCT and length of hospital stay (rs = -0.4, -0.2, P < 0.05) in infants with bacterial pneumonia. Conclusion: A low level of vitamin D is present in infants with bacterial pneumonia, and its status affects the severity and outcome of pneumonia. The level of LL-37 is increased in infants with bacterial pneumonia, but it shows a downward trend with progression of the disease.

Disentangling the Ecological Processes Shaping the Latitudinal Pattern of Phytoplankton Communities in the Pacific Ocean.

Phytoplankton diversity and community compositions vary across spaces and are fundamentally affected by several deterministic (e.g., environmental selection) and stochastic (e.g., ecological drift) processes. How this suite of different processes regulates the biogeography of phytoplankton remains to be comprehensively explored. Using high-throughput sequencing data and null model analysis, we revealed the ecological processes shaping the latitudinal community structure of three major phytoplankton groups (i.e., diatoms, Synechococcus, and haptophytes) across the Pacific Ocean (70°N, 170°W to 35°S, 170°W). At the basin scale, heterogeneous selection (selection under heterogeneous environmental conditions) dominated the assembly processes of all phytoplankton groups; however, its relative importance varied greatly at the climatic zonal scale, explaining the distinct latitudinal α- and ß-diversity among phytoplankton groups. Assembly processes in Synechococcus and haptophyte communities were mainly controlled by physical and nutrient factors, respectively. High temperature drove Synechococcus communities to be more deterministic with higher diversity, while haptophyte communities were less environmentally selected at low latitudes due to their wide niche breadth and mixotrophic lifestyle. Diatom communities were overwhelmingly dominated by the selection process but with low correlation of measured environmental factors to their community compositions. This could be attributed to the high growth rate of diatoms, as indicated by their lower site occupation frequency than predicted in the neutral community model. Our study showed that heterogeneous selection is the main force that shaped the biogeography of three key phytoplankton groups in the Pacific Ocean, with a latitudinal variation of relative importance due to the distinct traits among phytoplankton. IMPORTANCE Phytoplankton are diverse and abundant as primary producers in the ocean, with diversity and community compositions varying spatially. How fundamental processes (e.g., selection, dispersal, and drift) regulate their global biogeography remains to be comprehensively explored. In this study, we disentangled the ecological processes of three key phytoplankton groups (i.e., diatoms, Synechococcus, and haptophytes) along the same latitudinal gradients in the Pacific Ocean. Heterogeneous selection, by promoting species richness and reducing similarity between communities, was the dominant process shaping the communities of each phytoplankton group at the basin scale. However, its relative importance varied greatly among different phytoplankton groups in different climate zones, explaining the uneven latitudinal α- and ß-diversity. We also highlight the importance of identifying key factors mediating the relative importance of assembly processes in phytoplankton communities, which will enhance our understanding of their biogeography in the ocean and future patterns under climate changes.

Making comparable measurements of bacterial respiration and production in the subtropical coastal waters.

Accurate estimates of bacterial carbon metabolic rates are indispensable for understanding the regulation of carbon fluxes in aquatic environments. Here, changes in bacterial growth, production, and cell volume in both pre-filtered and unfiltered seawater during 24 h incubation were monitored. The methodological artifacts during Winkler bacterial respiration (BR) measurements in subtropical Hong Kong coastal waters were assessed. Bacterial abundance increased by 3- and 1.8-fold in the pre-filtered and unfiltered seawater after incubation, respectively. Bacterial production (BP) and cell volume also showed significant enhancement. Compared with the BR measurements obtained by the Winkler method, the instantaneous free-living BR measurements, after correction, decreased by ~ 70%. The time-integrated free-living BR and BP during 24 h incubation in the pre-filtered sample provided an improved estimate of bacterial growth efficiency, which increased by ~ 52% compared to the common estimations using the noncomparable measurements of integrated free-living BR and instantaneous total BP. The overestimation of BR also exaggerated the contribution of bacteria to community respiration, affecting the understanding on the metabolic state of the marine ecosystems. Furthermore, the BR estimates by the Winkler method may be more biased in environments with a higher bacterial growth rate and tightly coupled grazing mortality, as well as in those with higher nutrient concentrations. These results reveal obvious problems associated with the BR methodology and raise a warning for caution when comparing BP and BR, as well as when making estimations of carbon flow through the complex microbial networks in aquatic ecosystems. Supplementary Information: The online version contains supplementary material available at 10.1007/s42995-022-00133-2.

Blood glucose detection based on Teager-Kaiser main energy of photoacoustic signal.

Real-time blood glucose detection is an essential tool for diabetes monitoring. Non-invasive blood glucose detection technology is one of the current research hotspots in this field. Previous research mainly focused on improving the system's detection capability to obtain signals with low signal-to-noise ratio and high quality, and simple methods are often used in signal processing. Moreover, photoacoustic signal simulation also simplifies the influence of the transmission medium on the signal. In the present study, we built a new simulation model which considers human skin, blood, and the detector's limitations, to obtain a more practical photoacoustic signal. We then proposed a blood glucose detection algorithm based on Teager-Kaiser main energy (TKME) to overcome noise and medium interference and achieve a high detection accuracy at low SNR. Finally, the simulation and actual data were utilised during the experiment, and the detection error was 15 mg/dL (SNR = 10 dB).

Responses of marine phytoplankton communities to environmental changes: New insights from a niche classification scheme.

Predicting changes of phytoplankton communities in response to global warming is one of the challenges of ecological forecasting. One of the constraints is the paucity of general principles applicable to community ecology. Based on a synecological analysis of a decadal-scale database, we created a niche habitat classification scheme relating nine phytoplankton groups to fifteen statistically refined realized niches comprised of three niche dimensions: temperature, irradiance, and nitrate concentrations. The niche scheme assigned the nine phytoplankton groups to three types of niches: a cold type, a warm type, and a type associated with high irradiance and high nitrate concentrations. The fact that phytoplankton groups in cold niches were governed by irradiance and those in warm niches by nitrate is consistent with general ecological theories, but the fact that diatoms were the only dominant group in high-irradiance, high-nitrate niches challenges the idea based on autecological studies that diatoms are generally better adapted to low-irradiance, high-nutrient conditions. When combined with an irradiance model, the niche scheme revealed that photoinhibition of Prochlorococcus, which is predicted from autecological studies, is a function of temperature. We used the niche scheme to predict the responses of phytoplankton communities to environmental changes due to seawater warming and eutrophication. The results of the study suggest that a synecological analysis of large databases from field studies facilitates identification of general principles of community ecology that can be used to forecast responses of biological communities to environmental changes.

Effect of phytoplankton size diversity on primary productivity in the North Pacific: trait distributions under environmental variability.

While most biodiversity and ecosystem functioning (BEF) studies have found positive effects of species richness on productivity, it remain unclear whether similar patterns hold for marine phytoplankton with high local richness. We use the continuous trait-based modelling approach, which assumes infinite richness and represents diversity in terms of the variance of the size distribution, to investigate the effects of phytoplankton size diversity on productivity in a three-dimensional ocean circulation model driven by realistic physics forcing. We find a slightly negative effect of size diversity on primary production, which we attribute to several factors including functional trait-environment interactions, flexible stoichiometry and the saturation of productivity at low diversity levels. The benefits of trait optimisation, whereby narrow size distributions enhance productivity under relatively stable conditions, tend to dominate over those of adaptive capacity, whereby greater diversity enhances the ability of the community to respond to environmental variability.

Effects of increasing atmospheric CO2 on the marine phytoplankton and bacterial metabolism during a bloom: A coastal mesocosm study.

Increases of atmospheric CO2 concentrations due to human activity and associated effects on aquatic ecosystems are recognized as an environmental issue at a global scale. Growing attention is being paid to CO2 enrichment effects under multiple stresses or fluctuating environmental conditions in order to extrapolate from laboratory-scale experiments to natural systems. We carried out a mesocosm experiment in coastal water with an assemblage of three model phytoplankton species and their associated bacteria under the influence of elevated CO2 concentrations. Net community production and the metabolic characteristics of the phytoplankton and bacteria were monitored to elucidate how these organisms responded to CO2 enrichment during the course of the algal bloom. We found that CO2 enrichment (1000µatm) significantly enhanced gross primary production and the ratio of photosynthesis to chlorophyll a by approximately 38% and 39%, respectively, during the early stationary phase of the algal bloom. Although there were few effects on bulk bacterial production, a significant decrease of bulk bacterial respiration (up to 31%) at elevated CO2 resulted in an increase of bacterial growth efficiency. The implication is that an elevation of CO2 concentrations leads to a reduction of bacterial carbon demand and enhances carbon transfer efficiency through the microbial loop, with a greater proportion of fixed carbon being allocated to bacterial biomass and less being lost as CO2. The contemporaneous responses of phytoplankton and bacterial metabolism to CO2 enrichment increased net community production by about 45%, an increase that would have profound implications for the carbon cycle in coastal marine ecosystems.

Warming and eutrophication combine to restructure diatoms and dinoflagellates.

Temperature change and eutrophication are known to affect phytoplankton communities, but relatively little is known about the effects of interactions between simultaneous changes of temperature and nutrient loading in coastal ecosystems. Here we show that such interaction is key in driving diatom-dinoflagellate dynamics in the East China Sea. Diatoms and dinoflagellates responded differently to temperature, nutrient concentrations and ratios, and their interactions. Diatoms preferred lower temperature and higher nutrient concentrations, while dinoflagellates were less sensitive to temperature and nutrient concentrations, but tended to prevail at low phosphorus and high N:P ratio conditions. These different traits of diatoms and dinoflagellates resulted in the fact that both the effect of warming resulting in nutrients decline as a consequence of increasing stratification and the effect of increasing terrestrial nutrient input as a result of eutrophication might promote dinoflagellates over diatoms. We predict that conservative forecasts of environmental change by the year 2100 are likely to result in the decrease of diatoms in 60% and the increase of dinoflagellates in 70% of the surface water of the East China Sea, and project that mean diatoms should decrease by 19% while mean dinoflagellates should increase by 60% in the surface water of the coastal East China Sea. This analysis is based on a series of statistical niche models of the consequences of multiple environmental changes on diatom and dinoflagellate biomass in the East China Sea based on 2815 samples randomly collected from 23 cruises spanning 14 years (2002-2015). Our findings reveal that dinoflagellate blooms will be more frequent and intense, which will affect coastal ecosystem functioning.

Physical-Biological Coupling in the Western South China Sea: The Response of Phytoplankton Community to a Mesoscale Cyclonic Eddy.

It is widely recognized that the mesoscale eddies play an important part in the biogeochemical cycle in ocean ecosystem, especially in the oligotrophic tropical zones. So here a heterogeneous cyclonic eddy in its flourishing stage was detected using remote sensing and in situ biogeochemical observation in the western South China Sea (SCS) in early September, 2007. The high-performance liquid chromatography method was used to identify the photosynthetic pigments. And the CHEMical TAXonomy (CHEMTAX) was applied to calculate the contribution of nine phytoplankton groups to the total chlorophyll a (TChl a) biomass. The deep chlorophyll a maximum layer (DCML) was raised to form a dome structure in the eddy center while there was no distinct enhancement for TChl a biomass. The integrated TChl a concentration in the upper 100 m water column was also constant from the eddy center to the surrounding water outside the eddy. However the TChl a biomass in the surface layer (at 5 m) in the eddy center was promoted 2.6-fold compared to the biomass outside the eddy (p < 0.001). Thus, the slight enhancement of TChl a biomass of euphotic zone integration within the eddy was mainly from the phytoplankton in the upper mixed zone rather than the DCML. The phytoplankton community was primarily contributed by diatoms, prasinophytes, and Synechococcus at the DCML within the eddy, while less was contributed by haptophytes_8 and Prochlorococcus. The TChl a biomass for most of the phytoplankton groups increased at the surface layer in the eddy center under the effect of nutrient pumping. The doming isopycnal within the eddy supplied nutrients gently into the upper mixing layer, and there was remarkable enhancement in phytoplankton biomass at the surface layer with 10.5% TChl a biomass of water column in eddy center and 3.7% at reference stations. So the slight increasing in the water column integrated phytoplankton biomass might be attributed to the stimulated phytoplankton biomass at the surface layer.

Photoacoustic imaging of acupuncture effect in small animals.

Acupuncture has been a powerful clinical tool for treating chronic diseases. However, there is currently no appropriate method to clarify the therapeutic effect of acupuncture. Here, we use photoacoustic tomography (PAT) to study the effect of acupuncture on mouse brain blood vessels. Ten healthy mice were stimulated with acupuncture needles on two acupoints. PAT images were obtained before and after acupuncture. We report that stimulation of certain acupoints resulted in changes in hemodynamics/blood flow at these points. The results demonstrate that PAT can non-invasively detect blood flow changes in mouse brain under acupuncture. This pilot study shows the potential of PAT as a visualization tool for illuminating the mechanism of acupuncture and promoting its clinical applications.

Co-occurrence of phycocyanin- and phycoerythrin-rich Synechococcus in subtropical estuarine and coastal waters of Hong Kong.

Phylogenetic diversity of Synechococcus with different pigmentation in subtropical estuarine and coastal waters of Hong Kong was revealed by the phylogeny of cpcBA and cpeBA operons encoding for phycocyanin (PC) and phycoerythrin (PE). Synechococcus containing only PC (PC-rich Synechococcus) dominated at the estuarine station in summer, whereas PE-rich marine Synechococcus containing both PC and PE (PE-rich Synechococcus) dominated in the coastal waters. Our PC sequences are closely related to freshwater strains but differed from Baltic Sea strains, implying that they were from river discharge. Among PE-rich Synechococcus, clones grouping with strains containing only phycoerythrobilin (PEB-only) were abundant in July, while clones grouping with strains possessing a low content of phycourobilin (PUB) in addition to PEB (low PUB/PEB) were more abundant in January at both stations. Clones of high PUB/PEB types were only presented at the coastal station, but were not detected at the estuarine station. The much higher diversity of both PC-rich and PE-rich Synechococcus, as compared with the Baltic Sea, and the occurrence of the high PUB/PEB strains indicate the high dynamic nature of this subtropical estuarine-coastal environment with strong mixing of water masses ranging from Pearl River plume to oceanic South China Sea water. Our results of phylogenetic study agreed well with flow cytometric counts, which revealed the coexistence of PC-rich and PE-rich Synechococcus in the subtropical coastal waters and the dominance of the former type in the estuarine waters during summer high freshwater discharge. These results indicate that picocyanobacteria, particularly PC-rich Synechococcus, which has long been overlooked, are an important part of the primary production, and they could play an important role in the microbial food web in estuarine ecosystems.

[Mesocosm experiment on competition between two HAB species in East China Sea].

Skeletonema costatum and Prorocentrum dentatum are the two common HAB species in East China Sea, and Prorocentrum is more responsible for most HAB events in Spring since late 90's. The HAB caused by Skeletonema usually occurs from June to August. However, these two species will not bloom at the same time. Two mesocosm experiments were conducted in East China Sea in May 1998 and May 2002. In the experiment of May 1998, the cell number of Prorocentrum dentatum and Skeletonema costatum accounted for about 85% and 11% of total cell number of phytoplankton, respectively at the beginning of the experiment. In control mesocosm, Prorocentrum dentatum dominated the community during the whole experiment. In phosphate-enriched mesocosm, however, Skeletonema costatum showed a high competition capability. In May 2002, there were 4 bags in the mesocosm experiment. At the beginning of the experiment, the cell number of Prorocentrum dentatum accounted for 55-66% of the total, and that of Skeletonema costatum accounted for 32-42%. During the experiment, the growth of Skeletonema costatum was faster than that of Prorocentrum dentatum. On the 2nd day, the cell number of Skeletonema costatum exceeded that of Prorocentrum dentatum. It showed that under high nutrients conditions, Skeletonema costatum grew better than Prorocentrum dentatum, but under nutrients-limited conditions, Prorocentrum dentatum could survival better than Skeletonema costatum.