Flying over water: how “On bird species diversity” influenced aquatic ecology

Habitat complexity has long been known to influence animal community structure by increasing the number of available habitats. Fifty years have passed since MacArthur brothers published the seminal paper “On bird species diversity”, which revolutionized studies of habitat structure. This paper first evidenced and quantified the relationship between species diversity (birds) and habitat structural complexity (the number of stratified layers of landscape vegetation). In this article, we aim to pay homage to R. H. MacArthur’s contribution and to briefly analyze the citation history and influence of “On bird species diversity”, focusing primarily on aquatic studies. We searched for all papers that cited “On bird species diversity” on Thomson Reuters (ISI—Web of Knowledge) and analyzed them for temporal citation trends. In addition, considering only aquatic papers, we explored whether and how habitat complexity was measured, as well as the ecological organization level, attributes of organisms, taxonomic groups and study design (observational or experimental). “On bird species diversity” citations increased over time, but this paper was less cited by limnologists compared to terrestrial and marine scientists. The majority of investigations in aquatic ecosystems quantified habitat complexity, but few used mathematical modeling. The high number of citations, which continues to increase, shows the great influence of “On bird species diversity” on ecological studies and typifies it as a classic in the ecological literature. However, the low citation frequency found in papers devoted to freshwater ecosystems indicates that limnologists in general neglect this original contribution in studies of habitat complexity.     

Free-living nematodes research: State of the art,prospects, and future directions. A bibliometric analysis approach

Nematodes are among the most successful metazoans inhabiting the Earth and they are pivotal components as in terrestrial as in aquatic (both in marine and freshwater) environments providing important ecosystem services. The aim of this study was to understand major research trends and topics on free-living nematodes inhabiting soil, marine and freshwater environments and to highlight possible differences among them. To achieve this objective, a bibliometric analysis was performed using Scopus database. The indexed global scientific literature on free-living nematodes from 1912 to 2021 was explored using VOSviewer software, allowing a comprehensive overview of the topic. The analyses of co-authorship (among researchers and countries), the co-occurrence of keywords and the analysis of citation of journals were performed. Overall, free-living soil nematodes found a wider audience in high ranked journals especially when compared with freshwater nematodes. Marine nematodes stand in between them and many aspects of biodiversity research in marine ecosystems are covered by high-medium ranked journals (i.e. taxonomy, systematic, phylogeny, morphological and genetic diversity). Although, the estimation of the taxonomic diversity of the phylum Nematoda enumerated a high number of documents, an increasing attention emerged for the investigation of pollution effects (i.e. nematodes as bioindicators of environmental status) and the use of nematodes as model organisms for addressing scientific questions in line with the Eco-Evo-Devo (Ecological Evolutionary Developmental biology) approach. These fundamental themes were indirectly confirmed by the co-authorship analysis, which revealed that taking integrative approaches between taxonomy (both morphological and molecular), ecological and evolutionary aspects attracted a higher number of citations.     

The influence of “Homage to Santa Rosalia” on aquatic ecology: a scientometric approach

In 1959, G.E. Hutchinson provided a general explanation for the diversity of species in his paper “Homage to Santa Rosalia or why are there so many kinds of animals?” To assess the contribution of the ideas Hutchinson introduced in “The Homage” to aquatic ecology research, we performed a bibliometric evaluation of all the articles that cited this paper between 1960 and 2009. The articles were retrieved using the database from Thomson Reuters (ISI Web of Knowledge) in March 2009. For each paper, we first identified the studied environment (terrestrial, marine or freshwater) and whether the study was theoretical or empirical. For marine and freshwater studies, we recorded the journal where the article was published, the year of publication, the number of citations, the taxonomic group (e.g. fish, phytoplankton, zooplankton, macroinvertebrates or macrophytes), the habitat (e.g. wetlands, lakes, rivers, streams or ocean) and the main ideas addressed. A total of 1345 articles cited “The Homage”, and the number of citations increased significantly with time. Most of the articles that cited “The Homage” described research carried out in a terrestrial environment or were theoretical, and a lesser number of citations came from freshwater and marine papers, which used mainly fish and invertebrates as model organisms. In the aquatic sciences, most of the papers discussed the influences of competition and energy (productivity) on diversity. Our results indicate that “The Homage” can still be considered a “citation classic” and a breakthrough contribution, and that it is still having a great impact on different fields of ecology, including limnology and marine ecology.     

论文引用率影响因素——中外生态学期刊比较

本文选择8种有代表性中外生态学期刊,对其一定发表周期内的论文引用率进行分析,探讨生态学论文引用率的影响因素及中外生态学期刊的差异.结果表明：4种英文期刊的年均被引次数均远大于4种中文期刊;英文期刊1位作者的论文数量百分比相对较高;所有期刊的合著论文比例均较高,体现了合作性在现代生态学研究中的重要性;论文作者数量与引用率之间有一定的正相关关系,但不显著;英文期刊论文的长度显著高于中文论文;随着论文长度的增加,年均被引次数增多.对中外期刊论文的引用率变化动态进行分析表明,英文期刊中总被引次数高的论文其增长速率也较快,表明其持续影响力强于中文生态学论文.我们希望这些结果会对生态学者以及相关期刊工作者有所裨益.     

A multiproxy approach to inferring Holocene paleobotanical changes linked to sea-level variation,paleosalinity levels,and shallow lake alternative states in Negra Lagoon,SE Uruguay

A multiproxy analysis of diatoms, chrysophyte cysts, opal phytoliths, and palynomorphs was undertaken in Negra Lagoon, to decipher Holocene changes in paleobotanical proxies associated with sea-level changes and paleolimnological conditions. Before the Holocene transgression (7000 yr BP), a terrestrial system was inferred as no aquatic palynomorphs or biogenic silica remains were recorded. During the sea-level maximum (5200 yr BP), marine/brackish conditions were established as indicated by diatoms, Chenopodiaceae, and a high content of cysts of Peridinioideae. The catchment consisted of grasslands and wetlands as indicated by the opal phytolith data. The Holocene transgression was followed by a sea-level decrease, which led to the onset of brackish/freshwater conditions as inferred from the co-dominance of freshwater and marine/brackish diatoms. This is also supported not only by the concomitant increase in non-siliceous freshwater microalgae and emergent macrophytes, but also by the presence of Myriophyllum. As sea level continued to decrease during late Holocene, a freshwater system was observed because of the complete separation from the ocean. Chrysophyte cysts were consistently recorded and brackish diatoms exhibited reduced abundances. The observed limnological changes are consistent with the alternative states hypothesis of Scheffer’s model (1998). That is, the clear water phases were explained because of high macrophyte abundances, low phytoplankton frequencies, high cyst to diatom ratios, and increase in frequencies of benthic diatom species. Conversely, turbid phases were likely to occur when low cyst to diatom ratios together with increase in planktonic diatoms and decrease in macrophytes values were detected. This highlights the importance of this approach to detect long-term changes in shallow lake alternative states.     

Comparative genomics reveals insights into cyanobacterial evolution and habitat adaptation

Cyanobacteria are photosynthetic prokaryotes that inhabit diverse aquatic and terrestrial environments. However, the evolutionary mechanisms involved in the cyanobacterial habitat adaptation remain poorly understood. Here, based on phylogenetic and comparative genomic analyses of 650 cyanobacterial genomes, we investigated the genetic basis of cyanobacterial habitat adaptation (marine, freshwater, and terrestrial). We show: (1) the expansion of gene families is a common strategy whereby terrestrial cyanobacteria cope with fluctuating environments, whereas the genomes of many marine strains have undergone contraction to adapt to nutrient-poor conditions. (2) Hundreds of genes are strongly associated with specific habitats. Genes that are differentially abundant in genomes of marine, freshwater, and terrestrial cyanobacteria were found to be involved in light sensing and absorption, chemotaxis, nutrient transporters, responses to osmotic stress, etc., indicating the importance of these genes in the survival and adaptation of organisms in specific habitats. (3) A substantial fraction of genes that facilitate the adaptation of Cyanobacteria to specific habitats are contributed by horizontal gene transfer, and such genetic exchanges are more frequent in terrestrial cyanobacteria. Collectively, our results further our understandings of the adaptations of Cyanobacteria to different environments, highlighting the importance of ecological constraints imposed by the environment in shaping the evolution of Cyanobacteria.Subject terms: Phylogenetics, Microbial ecology     

Nucleopolyhedrovirus Detection and Distribution in Terrestrial,Freshwater, and Marine Habitats of Appledore Island,Gulf of Maine

Viruses in aquatic ecosystems comprise those produced by both autochthonous and allochthonous host taxa. However, there is little information on the diversity and abundance of viruses of allochthonous origin, particularly from non-anthropogenic sources, in freshwater and marine ecosystems. We investigated the presence of nucleopolyhedroviruses (NPV) (Baculovirus), which commonly infect terrestrial lepidopteran taxa, across the landscape of Appledore Island, Gulf of Maine. PCR and qPCR primers were developed around a 294-bp fragment of the polyhedrin (polH) gene, which is the major constituent protein of NPV multivirion polyhedral occlusion bodies. polH was successfully amplified from several aquatic habitats, and recovered polH sequences were most similar to known lepidopteran NPV. Using quantitative PCR designed around a cluster of detected sequences, we detected polH in Appledore Island soils, supratidal freshwater ponds, nearshore sediments, near- and offshore plankton, and in floatsam. This diverse set of locations suggests that NPVs are widely dispersed along the terrestrial—marine continuum and that free polyhedra may be washed into ponds and eventually to sea. The putative hosts of detected NPVs were webworms (Hyphantria sp.) which form dense nests in late summer on the dominant Appledore Island vegetation (Prunus virginiana). Our data indicate that viruses of terrestrial origin (i.e., allochthonous viruses) may be dispersed widely in coastal marine habitats. The dispersal of NPV polH and detection within offshore net plankton (>64 μm) demonstrates that terrestrial viruses may interact with larger particles and plankton of coastal marine ecosystem, which further suggests that viral genomic information may be transported between biomes.     

The First Freshwater Mosasauroid (Upper Cretaceous,Hungary) and a New Clade of Basal Mosasauroids

Mosasauroids are conventionally conceived of as gigantic, obligatorily aquatic marine lizards (1000s of specimens from marine deposited rocks) with a cosmopolitan distribution in the Late Cretaceous (90–65 million years ago [mya]) oceans and seas of the world. Here we report on the fossilized remains of numerous individuals (small juveniles to large adults) of a new taxon, Pannoniasaurus inexpectatus gen. et sp. nov. from the Csehbánya Formation, Hungary (Santonian, Upper Cretaceous, 85.3–83.5 mya) that represent the first known mosasauroid that lived in freshwater environments. Previous to this find, only one specimen of a marine mosasauroid, cf. Plioplatecarpus sp., is known from non-marine rocks in Western Canada. Pannoniasaurus inexpectatus gen. et sp. nov. uniquely possesses a plesiomorphic pelvic anatomy, a non-mosasauroid but pontosaur-like tail osteology, possibly limbs like a terrestrial lizard, and a flattened, crocodile-like skull. Cladistic analysis reconstructs P. inexpectatus in a new clade of mosasauroids: (Pannoniasaurus (Tethysaurus (Yaguarasaurus, Russellosaurus))). P. inexpectatus is part of a mixed terrestrial and freshwater faunal assemblage that includes fishes, amphibians turtles, terrestrial lizards, crocodiles, pterosaurs, dinosaurs and birds.     

Species Distribution Models and Impact Factor Growth in Environmental Journals: Methodological Fashion or the Attraction of Global Change Science

In this work, I evaluate the impact of species distribution models (SDMs) on the current status of environmental and ecological journals by asking the question to which degree development of SDMs in the literature is related to recent changes in the impact factors of ecological journals. The hypothesis evaluated states that research fronts are likely to attract research attention and potentially drive citation patterns, with journals concentrating papers related to the research front receiving more attention and benefiting from faster increases in their impact on the ecological literature. My results indicate a positive relationship between the number of SDM related articles published in a journal and its impact factor (IF) growth during the period 2000–09. However, the percentage of SDM related papers in a journal was strongly and positively associated with the percentage of papers on climate change and statistical issues. The results support the hypothesis that global change science has been critical in the development of SDMs and that interest in climate change research in particular, rather than the usage of SDM per se, appears as an important factor behind journal IF increases in ecology and environmental sciences. Finally, our results on SDM application in global change science support the view that scientific interest rather than methodological fashion appears to be the major driver of research attraction in the scientific literature.     

What determines the citation frequency of ecological papers?

Citation frequencies of scientific articles are increasingly used for academic evaluation in various disciplines, including ecology. However, the factors affecting citation rates have not been extensively studied. Here, we examine the association between the citation frequency of ecological articles and various characteristics of journals, articles and authors. Our analysis shows that the annual citation rates of ecological papers are affected by the direction of the study outcome with respect to the hypothesis tested (supportive versus unsupportive evidence), by article length, by the number of authors, and by their country and university of affiliation. These results cast doubt on the validity of using citation counts as an objective and unbiased tool for academic evaluation in ecology.     

Biodiversity effects on ecosystem functioning: insights from aquatic systems

Unprecedented rates of species extinctions have prompted extensive research into the consequences of biodiversity losses on ecosystem functioning. While aquatic species are most threatened, research with freshwater and marine model systems has lagged behind progress made in terrestrial environments. This editorial to a special feature summarizes the main outcomes of a conference aimed at setting the stage for exploring the potential of aquatic systems to assess the role of biodiversity in ecosystem functioning. This series of papers proposes fresh approaches to the study of biodiversity effects on ecosystem functioning, outlines a new way of analyzing experimental data, presents a model that considers scale as an important factor determining outcomes, explores the effects of multiple stressors on species richness and ecosystem processes, and develops a food-web perspective that relates ecosystem properties to biodiversity. An insightful synthesis of lessons learned from aquatic systems is premature at present, but the papers clearly demonstrate the role that marine and freshwater systems can play in resolving open questions. The implications go well beyond the biodiversity in, and functioning of, ecosystems shaped by free-flowing or standing water.     

Algal Taxonomy in Limnology: An Example of the Declining Trend of Taxonomic Studies?

The recent decline in taxonomic studies is well recognized. Algae-related papers (390) published in five leading limnology journals (1971–2004) were consulted to assess similar trends in limnology by taking algae as a test aquatic group. The study showed a decrease of algae-only studies and an increase of multi-group studies (algae plus one or more aquatic groups). Identification of species decreased while mentioning of ecological groups (phytoplankton, epiphytes, etc.) increased while presenting results. Species identification, however, was not associated with number of aquatic groups or number of algal species included in a study. Problems probably lie with the old-fashioned image of taxonomy and it being threatened by the recent advancement in evolutionary and molecular biology. Issues like the changing research patterns in freshwater ecology, scope of limnological works, its workers and relevant journals are also shaping the status of traditional taxonomy in limnology. Practices such as giving of at least (algal) genera in community studies, and of the current names of studied species in physiological/molecular works and also in studies on particular supra-generic taxa (Class, Family, etc.), could help sustaining of taxonomy in limnology.     

Optimized isolation procedure for obtaining strongly actinide binding exopolymeric substances (EPS) from two bacteria (Sagittula stellata and Pseudomonas fluorescens Biovar II)

Different chemical extractants (NaCl, EDTA, HCl and NaOH) and physical methods (ultrasonication and heating) were examined by their efficacies of extracting “attached” exopolymeric substances (EPS) secreted by marine bacterium Sagittula stellata (SS) and terrestrial bacterium Pseudomonas fluorescens Biovar II (PF). Extraction by 0.5 N HCl for 3 h was best for SS while extraction by 0.05 N NaCl for 3–5 h was regarded as optimal for PF. Improvements in EPS purification included a pre-diafiltration step to remove the broth material and reduce the solution volume, thus the usage of ethanol, and time. The EPS harvested at the optimal time and purified by the improved method were enriched in polysaccharides, with smaller amounts of proteins, thus having amphiphilic properties. Isoelectric focusing of ²³⁴Th or ²⁴⁰Pu labeled EPS showed both actinides were strongly bound to macromolecules with low pI, similar to reported marine or soil colloidal natural organic matter (NOM).     

Trends and prospects for local knowledge in ecological and conservation research and monitoring

Local ecological knowledge (LEK) of those who earn their livelihoods from natural environments has long been recognized as providing far-reaching insights into ecological processes. It is being increasingly used by ecologists to address diverse questions that often focus on applied conservation issues and may incorporate local knowledge with biological data from more conventional research and monitoring. We characterize how LEK has been used in the ecological and conservation literature over the last 25 years by broadly examining 360 journals and by evaluating 12 prominent ecological and conservation journals in greater detail. Over this period, the use of LEK has increased considerably, although only 0.01% of papers in the broad and 0.42% of those in the more detailed evaluation incorporated LEK. Despite this increase, LEK-based publications remain nearly absent from the more established theoretical literature and are largely restricted to more recent and arguably less prestigious applied and interdisciplinary journals. Most LEK studies used interviews, but generally failed to actively include community members in the research process. Changes to the research and publishing process that include local people and address these shortcomings and the broader issues of power and influence in the sciences are critical to the successful utilization of LEK. These changes are necessary for the appropriate depiction of these knowledge systems and to ensure that local knowledge holders will continue participating in ecological research aimed at conservation.     

Hexapoda phylogeny: implications for an aquatic origin hypothesis

Emergence from an aquatic environment to the land is one of the major evolutionary transitions within the arthropods. It is often considered that the first hexapods, and especially the first Collembola, went from the sea through intermediate freshwater environments to colonize fully terrestrial ecosystems. To understand the ancestral ecology of hexapods, a phylogenetic framework is used. By mapping ecological attributes onto the phylogeny, it is shown that hexapods colonized terrestrial environments directly from marine environment without a transition through freshwater. An edaphic life-style is the basal state for Collembola and more generally for hexapods as a whole. Aquatic ecology is inferred to be a secondary change that occurred several times independently, particularly in some group of Collembola and Pterygota. The answer is ambiguous for Pterygota, whether the first Pterygota had aquatic larvae and reversed toward fully terrestrial in Neoptera, or aquatic larvae appeared independently in Odonata and Ephemeroptera. Subsequently, aquatic larvae were secondarily acquired in various groups independently (e.g. Plecoptera, Trichoptera, Coleoptera).     

Ecological functions of volatile organic compounds in aquatic systems

In terrestrial ecosystems, volatile organic compounds (VOCs) are widely acknowledged as an important group of infochemicals. They play a major role in pollinator attraction by terrestrial plants and as insect pheromones. Furthermore, they are the mediating agent of so-called 'tritrophic interactions'. When plants are attacked by herbivorous insects, volatile signal substances are emitted, which act as attractants for parasitoids that kill the herbivores, thereby protecting the plant from herbivory. Despite the generally acknowledged importance of VOCs in terrestrial chemical ecology, their functions in aquatic food webs are largely unknown. VOCs produced by algae and cyanobacteria are a major concern in water processing, since aquatic primary producers are the reason for regularly encountered taste and odour problems in drinking water. Only very recently, research in aquatic chemical ecology has started to investigate possible ecological functions for the production of VOCs by algae and cyanobacteria. Volatile aldehydes released by wounded cells of marine planktonic diatoms seem to act as defensive compounds against herbivorous copepods on the population level. Just recently, it was found that VOCs released from benthic algae and cyanobacteria can be utilised as food and/or habitat finding cues by aquatic invertebrates such as freshwater gastropods and nematodes. Here, I review concepts and recent experimental studies on the ecological functions of such VOCs in aquatic ecosystems. Understanding the factors that lead to the liberation of volatile compounds is an essential prerequisite to properly assessing their ecological functions. It appears that (similar to terrestrial plant-herbivore interactions) VOCs can also play a steering role for both attraction and defence in aquatic ecosystems.     

A meta‐analysis of the effects of detritus on primary producers and consumers in marine,freshwater, and terrestrial ecosystems

Detritus is a central feature in marine, freshwater, and terrestrial ecosystems. Despite the ubiquity of detritus, ecologists have largely ignored its role in influencing food web structure. We used a meta‐analytic approach to ask three questions about how detritus affects food web structure in a wide variety of ecosystems. First, what is the effect strength of detritus on primary producers, detritivores, herbivores, and predators? Second, what functional role does detritus serve for consumers (energetic, habitat, or both)? Third, how does the effect of detritus on consumers vary between aquatic and terrestrial ecosystems? We found that detritus has strong positive effects on primary producers and consumers in a wide range of ecosystems types. Detritus has a positive direct effect on detritivores by providing both an energetic resource and habitat (refuge from predators). Detritus has equally strong positive effects on herbivores and predators, driven by a positive direct effect of habitat. Detritus has positive effects on consumers in both aquatic and terrestrial ecosystems with 1.7 times stronger effects in terrestrial ecosystems. These results suggest that detritus has strong effects on food‐web structure in a variety of ecosystem types. Even the portion of the food web that is linked most strongly to living plant tissue as its primary energy source is strongly positively affected.