Experimental analysis of patch dynamics in tallgrass prairie plant communities

Abstract. Previous research has indicated that patch structure at small spatial scales (<100m²) in tallgrass prairies was defined by a diverse array of infrequent species because dominant species occurred in all samples at this scale. Also, patch structure was not significantly different from that derived from random species associations. Based on these results, we hypothesized that remo val of a dominant species would have no effect on patch structure in these prairies. We tested this hypothesis by removing a dominant grass, Schizachyrium scoparium (Poaceae), from half of each of four 10 m × 10 m study blocks, and comparing differences in patch structure between control and removal halves before and after removal. The minimum resolution in our study was 1 m². Patches of similar species composition were defined by cluster analysis of presence/absence data and cover data. Patch sizes ranged from 1 to 34 m². Following the removal of S. scoparium there was an overall increase in the number of species in the removal half of each block compared to pre-treatment levels. However, the number of patch types and number of spatially mapped groups, based on presence/absence or cover data, did not change between control and removal plots after the removal of S. scoparium. This supports the hypothesis that removal of a large, dominant species would have no effect on patch structure at this scale of resolution in these prairies. Thus, patch structure, as defined here, is an emergent property in these grasslands that is not predictable from changes in species composition. This property of stochastic patch structure results from interactions of processes operating at scales both larger and smaller than our scale of resolution. Stochastic models may provide a reasonable approach to modelling small-scale patch dynamics in tallgrass prairie communities.     

Disentangling the historical routes to community assembly in the global epicentre of biodiversity

Aim

The exceptional turnover in biota with elevation and number of species coexisting at any elevation makes tropical mountains hotspots of biodiversity. However, understanding the historical processes through which species arising in geographical isolation (i.e. allopatry) assemble along the same mountain slope (i.e. sympatry) remains a major challenge. Multiple models have been proposed including (1) the sorting of already elevationally divergent species, (2) the displacement of elevation upon secondary contact, potentially followed by convergence, or (3) elevational conservatism, in which ancestral elevational ranges are retained. However, the relative contribution of these processes to generating patterns of elevational overlap and turnover is unknown.

Location

Tropical mountains of Central- and South-America.

Time Period

The last 12 myr.

Major Taxa Studied

Birds.

Methods

We collate a dataset of 165 avian sister pairs containing estimates of phylogenetic age, geographical and regional elevational range overlap. We develop a framework based on continuous-time Markov models to infer the relative frequency of different historical pathways in explaining present-day overlap and turnover of sympatric species along elevational gradients.

Results

We show that turnover of closely related bird species across elevation can predominantly be explained by displacement of elevation ranges upon contact (81%) rather than elevational divergence in allopatry (19%). In contrast, overlap along elevation gradients is primarily (88%) explained by conservatism of elevational ranges rather than displacement followed by elevational expansion (12%).

Main Conclusions

Bird communities across elevation gradients are assembled through a mix of processes, including the sorting, displacement and conservatism of species elevation ranges. The dominant role of conservatism in explaining co-occurrence of species on mountain slopes rejects more complex scenarios requiring displacement followed by expansion. The ability of closely related species to coexist without elevational divergence provides a direct and faster pathway to sympatry and helps explain the exceptional species richness of tropical mountains.     

大陈岛海域浮游动物群落季节变化及其影响因素

为探究大陈岛海域浮游动物群落的季节变化,于2020年9月（夏季）、11月（秋季）和2021年1月（冬季）、4月（春季）分别对大陈岛海域的浮游动物及环境因子进行了4个航次的调查。结果共鉴定浮游动物90种,包括浮游幼体15类,其中夏季种类数最多（68种）,冬季最少（20种）,常见的优势种有：百陶箭虫（Sagitta bedoti）、微刺哲水蚤（Canthocalanus pauper）、中华哲水蚤（Calanus sinicus）等12种（Y>0.02）。浮游动物的年平均丰度和生物量分别为（153.40±214.73）个/m³、（411.93±561.76） mg/m³,二者存在明显的季节变化,平均丰度为春季（380.17±296.14）个/m³>夏季（135.30±112.59）个/m³>秋季（67.88±90.52）个/m³>冬季（25.30±19.11）个/m³;平均生物量为夏季（895.01±802.54） mg/m³>春季（623.39±358.73） mg/m³>秋季（91.08±82.36） mg/m³>冬季（45.96±84.95） mg/m³。多样性指数（H''）和均匀度指数（J''）的年平均值分别为1.71±0.96和0.53±0.20,均表现出夏秋季较高、冬春季较低的特征。聚类分析结果表明调查海域的浮游动物可划分为夏季类群、秋季类群、冬季类群和春季类群4组类群。Pearson相关性分析和冗余分析（RDA）结果表明,海水温度、盐度、叶绿素a浓度是影响大陈岛海域浮游动物群落特征的重要环境因素。此外,夏季大陈岛海域水母类浮游动物暴发的现象值得关注。研究结果将为大陈岛海域的生物多样性保护及渔业资源可持续开发利用提供可参考的数据资料。     

Structural insights into thermostable direct hemolysin of Vibrio parahaemolyticus using single-particle cryo-EM

Thermostable direct hemolysin (TDH) is a ~19 kDa, hemolytic pore-forming toxin from the gram-negative marine bacterium Vibrio parahaemolyticus, one of the causative agents of seafood-borne acute gastroenteritis and septicemia. Previous studies have established that TDH exists as a tetrameric assembly in physiological state; however, there is limited knowledge regarding the molecular arrangement of its disordered N-terminal region (NTR)—the absence of which has been shown to compromise TDH's hemolytic and cytotoxic abilities. In our current study, we have employed single-particle cryo-electron microscopy to resolve the solution-state structures of wild-type TDH and a TDH construct with deletion of the NTR (NTD), in order to investigate structural aspects of NTR on the overall tetrameric architecture. We observed that both TDH and NTD electron density maps, resolved at global resolutions of 4.5 and 4.2 Å, respectively, showed good correlation in their respective oligomeric architecture. Additionally, we were able to locate extra densities near the pore opening of TDH which might correspond to the disordered NTR. Surprisingly, under cryogenic conditions, we were also able to observe novel supramolecular assemblies of TDH tetramers, which we were able to resolve to 4.3 Å. We further investigated the tetrameric and inter-tetrameric interaction interfaces to elaborate upon the key residues involved in both TDH tetramers and TDH super assemblies. Our current structural study will aid in understanding the mechanistic aspects of this pore-forming toxin and the role of its disordered NTR in membrane interaction.     

High diversity and low specificity of fungi associated with seedless epiphytic plants

Epiphytes, which grow on other plants for support, make up a large portion of Earth's plant diversity. Like other plants, their surfaces and interiors are colonized by diverse assemblages of fungi that can benefit their hosts by increasing tolerance for abiotic stressors and resistance to disease or harm them as pathogens. Fungal communities associated with epiphytic plants and the processes that structure these communities are poorly known. To address this, we sampled seven epiphytic seedless plant taxa in a Costa Rican rainforest and examined the effects of host identity and microhabitat on external and endophytic fungal communities. We found low host specificity for both external and endophytic fungi and weak differentiation between epiphytic and neighboring epilithic plant hosts. High turnover in fungi within and between hosts and habitats reveals that epiphytic plant-associated fungal communities are highly diverse and suggests that they are structured by stochastic processes.     

Selection of synthetic proteins to modulate the human frataxin function

Frataxin is a kinetic activator of the mitochondrial supercomplex for iron-sulfur cluster assembly. Low frataxin expression or a decrease in its functionality results in Friedreich's Ataxia (FRDA). With the aim of creating new molecular tools to study this metabolic pathway, and ultimately, to explore new therapeutic strategies, we have investigated the possibility of obtaining small proteins exhibiting a high affinity for frataxin. In this study, we applied the ribosome display approach, using human frataxin as the target. We focused on Affi_224, one of the proteins that we were able to select after five rounds of selection. We have studied the interaction between both proteins and discussed some applications of this specific molecular tutor, concerning the modulation of the supercomplex activity. Affi_224 and frataxin showed a K_D value in the nanomolar range, as judged by surface plasmon resonance analysis. Most likely, it binds to the frataxin acidic ridge, as suggested by the analysis of chemical shift perturbations (nuclear magnetic resonance) and computational simulations. Affi_224 was able to increase Cys NFS1 desulfurase activation exerted by the FRDA frataxin variant G130V. Importantly, Affi_224 interacts with frataxin in a human cellular model. Our results suggest quaternary addition may be a new tool to modulate frataxin function in vivo. Nevertheless, more functional experiments under physiological conditions should be carried out to evaluate Affi_224 effectiveness in FRDA cell models.     

Neo-tropical felid activity patterns in relation to potential prey and intraguild competitors in the Calakmul Biosphere Reserve,Mexico

Predator behaviors influence, and are influenced by, prey and competitor behaviors. Jaguars (Panthera onca), pumas (Puma concolor), and ocelots (Leopardus pardalis) coexist throughout their geographic range as the three largest predators in a multi-predator community across diverse environments. This study tested for non-random segregation and overlap in the activity patterns of these felids and their shared prey in the southern buffer zone of the Calakmul Biosphere Reserve, in southern Mexico, using camera traps during February to August 2019. We detected little temporal segregation between the nocturnal activities of jaguars, pumas, and ocelots, although pumas were more active closer to dawn. Jaguars had low activity overlap with species likely to be common prey, whereas ocelots had high overlap with their potential prey. Pumas displayed finer-scale similarities in activity with species likely to be common prey. In an understudied area of conservation importance, this study shows that temporal segregation is an unlikely mechanism of coexistence. Further research should incorporate spatio-temporal avoidance and dietary differences to improve our understanding of the mechanisms that drive coexistence between generalist species in a diverse assemblage of threatened felids. Abstract in Spanish is available with online material.     

Effects of media composition on substrate removal by pure and mixed bacterial cultures

Continuous culture experiments with identical experimental designs were run with a mixed microbial community of activated sludge origin and an axenic bacterial culture derived from it. Each culture received 2-chlorophenol (2-CP) at a concentration of 160 mg/L as COD and L-lysine at a concentration of 65 mg/L as COD. A factorial experimental design was employed with dilution rate and media composition as the two controlled variables. Three dilution rates were studied: 0.015, 0.0325, and 0.05 h^–1. Media composition was changed by adding four biogenic compounds (butyric acid, thymine, glutamic acid and lactose) in equal COD proportions at total concentrations of 0, 34, 225, and 1462 mg/L as COD. The measured variables were the effluent concentrations of 2-CP as measured by the 4-aminoantipyrene test and lysine as measured by the o-diacetylbenzene procedure. The results suggest that community structure and substrate composition play important roles in the response of a microbial community to mixed substrates. The addition of more biogenic substrates to the axenic culture had a deleterious effect on the removal of both lysine and 2-CP, although the effect was much larger on lysine removal. In contrast, additional substrates had a positive effect on the removal of 2-CP by the mixed community and much less of a negative effect on the removal of lysine. The dilution rate at which the cultures were growing had relatively little impact on the responses to the additional substrates.Abbreviations COD chemical oxygen demand - 2-CP 2-chlorophenol - DOC dissolved organic carbon - MDL method detection limit - SS suspended solids