The influence of primer choice on archaeal phylogenetic analyses based on 16S rRNA gene PCR

Polymerase chain reaction (PCR) assays targeting 16S rRNA genes followed by DNA sequencing are still important tools to characterize microbial communities present in environmental samples. However, despite the crescent number of deposited archaeal DNA sequences in databases, until now we do not have a clear picture of the effectiveness and specificity of the universal primers widely used to describe archaeal communities from different natural habitats. Therefore, in this study, we compared the phylogenetic profile obtained when Cerrado lake sediment DNA samples were submitted to 16S rDNA PCR employing three Archaea-specific primer sets commonly used. Our findings reveal that specificity of primers differed depending on the source of the analyzed DNA. Furthermore, archaeal communities revealed by each primer pair varied greatly, indicating that 16S rRNA gene primer choice affects the community profile obtained, with differences in both taxon detection and operational taxonomic unit (OTU) estimates.

МОДЕЛЮВАННЯ ЧИСЕЛЬНОСТІ ГРИЗУНІВ У ЛІСОВИХ БІОТОПАХ ЗАХІДНОГО ПОДІЛЛЯ (НА ПРИКЛАДІ MYODES GLAREOLUS)

Monitoring and predicting the dynamics of abundance of species living in natural habitats is an important component stability analysis of ecosystem as well as dynamics and direction of change of biotic communities under global climate change and pressure of the alien species. The aim of the work was to build a matrix model and study the state of stabilisation of the dynamics of the bank vole population within the Leslie model. The object of the study was the population dynamics of Myodes glareolus Schreber, 1780 = Clethrionomys glareolus auct. The study is based on materials obtained during 2017–2019. This period covered one phase of the long-term population dynamics of the bank vole, named “population growth”. The research was carried out according to generally accepted methods. A total of 6400 trap-days were processed, and 358 forest fistulas were collected and studied. The intensity of harmful activity of rodents is due to the variability of the number of animals in the population. The quantitative population changes are the result of three factors: births, deaths, and migrations. The main condition for the existence of the species is the stability of the population, which is determined by the action of thecompensatory mechanisms. The growth phase of the bank vole lasted all three years of the research, the quantitative indicators were respectively: 2017 – 1.8 individuals per 100 trap-days; 2018 – 2.0 individuals per 100 trap-days; 2019 – 2.7 individuals per 100 trap-days. Low levels of the abundance in the spring of each year of the study, namely at the beginning of the breeding season (3.7 – 2.6 – 8.9 individuals per 100 trap-days). Favourable for the abundance growth was the sex ratio of the population (approximately 1:1), with some rise in the share of females, which decreases on the period of spring 2018 to autumn 2019). Some decrease in the share of immature individuals (4.5 – 3.9 – 3.1 %) is an indirect confirmation of the stability of puberty of animals with subsequent replenishment of the "stock", which led to accelerated reproduction and, consequently, provided prerequisites for further population growth. The causal mechanisms of population control established by us, without a doubt, can serve as a basis for further prognosis, of the number of pests in natural habitats. To predict population changes, the Leslie model, which is widely used in mathematical analyses of the abundance of both plant and animal groups, was chosen. The algorithm for building a matrix model, detailed in the article, has five following steps. The exponential nature of the actual and projected growth of the bank vole population during the five-year cycle (2017–2019 with a prognosis until 2023) revealed in the analysis can be explained not so much by the power of the species' reproductive potential as by the lack of the significant changes in habitat, caused by constant weather conditions, low individual mortality from predators and non-communicable diseases or other accidents. The application of the matrix model allowed to confirm the key role of the main compensatory mechanisms of population dynamics, as they contribute to the stabilisation of the population and, as a consequence, are an important condition for the existence of the species.

Phytoremediation as an effective tool to handle emerging contaminants

Phytoremediation is a process which effectively uses plants as a tool to remove, detoxify or immobilize contaminants. It has been an eco-friendly and cost-effective technique to clean contaminated environments. The contaminants from various sources have caused an irreversible damage to all the biotic factors in the biosphere. Bioremediation has become an indispensable strategy in reclaiming or rehabilitating the environment that was damaged by the contaminants. The process of bioremediation has been extensively used for the past few decades to neutralize toxic contaminants, but the results have not been satisfactory due to the lack of cost-effectiveness, production of byproducts that are toxic and requirement of large landscape. Phytoremediation helps in treating chemical pollutants on two broad categories namely, emerging organic pollutants (EOPs) and emerging inorganic pollutants (EIOPs) under in situ conditions. The EOPs are produced from pharmaceutical, chemical and synthetic polymer industries, which have potential to pollute water and soil environments. Similarly, EIOPs are generated during mining operations, transportations and industries involved in urban development. Among the EIOPs, it has been noticed that there is pollution due to heavy metals, radioactive waste production and electronic waste in urban centers. Moreover, in recent times phytoremediation has been recognized as a feasible method to treat biological contaminants. Since remediation of soil and water is very important to preserve natural habitats and ecosystems, it is necessary to devise new strategies in using plants as a tool for remediation. In this review, we focus on recent advancements in phytoremediation strategies that could be utilized to mitigate the adverse effects of emerging contaminants without affecting the environment.

The current state of the introduction coenopopulation of Gymnospermium odessanum on the botanical-geographical plot “Steppes of Ukraine” at the M. M. Gryshko National Botanical Garden of the NAS of Ukraine

Gymnospermium odessanum is a rare relict endemic plant species. The research was carried out during G. odessanum flowering in 2019–2021 at the botanical-geographical plot “Steppes of Ukraine” of the M.M. Gryshko National Botanical Garden, National Academy of Sciences of Ukraine (NBG). Ecological and coenotic conditions of introduction at the NBG differ from natural habitats of the species and are not optimal for its vegetation. However, this species demonstrated ecological-coenotic plasticity and, over the decades, has formed a stable homeostatic introduction coenopopulation here. As of 2021, the area of introduction coenopopulation of G. odessanum at the NBG was 2,075 m2. It comprises 412 individuals of this species (including 40 seedlings, 241 juvenile, 45 immature, 40 virginal, 45 generative, and 1 sub-senile plants). Coenopopulation fragments with a high density of G. odessanum individuals are rare here, so the average density is low – only 0.2 individuals per 1 m2. In 2021, in the spectrum of age states, the total percentage of pregenerative individuals was very high and reached 88.8 %; the share of generative individuals was 10.9 %.In general, the age structure of the introduction coenopopulation of G. odessanum is characterized by long-term (2010–2021) stability. The spatial distribution of individuals in the introduction coenopopulation is of two kinds – random and in groups. This is due to combined myrmecochoric and barochoric propagation. Also due to myrmecochory, this coenopopulation tends to spread the area. Compared to natural coenopopulations, the introduction coenopopulation of G. odessanum at the NBG is characterized by a larger area, a much significant number, and, at the same time, a low average density of individuals. However, like in most of natural populations, its age spectrum is left-sided.The conducted research testifies the successful formation of the introduction coenopopulation of G. odessanum in the meadow-steppe cultural phytocoenosis of the NBG. This introduction coenopopulation is an example of a successful multi-year scientific experiment and effective ex situ protection and preservation of G. odessanum on the northern border of the Right Bank Forest-Steppe of Ukraine, far beyond the natural range of this endemic plant species.

Underwater Video as a Tool to Quantify Fish Density in Complex Coastal Habitats

Habitat loss is a serious issue threatening biodiversity across the planet, including coastal habitats that support important fish populations. Many coastal areas have been extensively modified by the construction of infrastructure such as ports, seawalls, docks, and armored shorelines. In addition, habitat restoration and enhancement projects often include constructed breakwaters or reefs. Such infrastructure may have incidental or intended habitat values for fish, yet their physical complexity makes quantitatively sampling these habitats with traditional gears challenging. We used a fleet of unbaited underwater video cameras to quantify fish communities across a variety of constructed and natural habitats in Perdido and Pensacola Bays in the central northern Gulf of Mexico. Between 2019 and 2021, we collected almost 350 replicate 10 min point census videos from rock jetty, seawall, commercial, public, and private docks, artificial reef, restored oyster reef, seagrass, and shallow sandy habitats. We extracted standard metrics of Frequency of Occurrence and MaxN, as well as more recently developed MeanCount for each taxon observed. Using a simple method to measure the visibility range at each sampling site, we calculated the area of the field of view to convert MeanCount to density estimates. Our data revealed abundant fish assemblages on constructed habitats, dominated by important fisheries species, including grey snapper Lutjanus griseus and sheepshead Archosargus probatocephalus. Our analyses suggest that density estimates may be obtained for larger fisheries species under suitable conditions. Although video is limited in more turbid estuarine areas, where conditions allow, it offers a tool to quantify fish communities in structurally complex habitats inaccessible to other quantitative gears.

Two Shades of Grey: Effect of Temperature on Seed Germination of the Escaping Ornamental Species Lychnis Coronaria and Stachys Byzantina

This paper describes germination and cytological variability in two popular ornamental and potentially invasive species, lamb’s ear Stachys byzantina and rose campion Lychnis coronaria. Both xerophytic species have the potential to invade natural habitats across Europe and create viable naturalised populations, with subsequent impacts on native vegetation. To assess the species’ invasiveness, seeds were collected from naturalised populations and germination rate recorded under different temperature regimes. Flow cytometry, used to record cytological variability, indicated that all populations of both species were cytologically homogeneous. Germination success, a key spreading factor in both species, was significantly influenced by temperature, with final germination of L. coronaria being extremely high at temperatures > 15/10 °C (98.5%) and extremely low at temperatures < 10/5 °C (2.9%). In comparison, final germination in S. byzantina highest at 22/15 °C (55.6%), reducing to 40.3% at 15/10 °C and just 0.3% at temperatures < 10/5 °C. No significant differences in germination rate were observed between escaping and non-escaping populations, though there were differences between particular populations. Our results indicate germination temperature limits between species consistent with sizes of primary distribution and distance between primary and secondary distribution borders. However, the observed germination rates allow for successful generative reproduction of both species over their secondary distribution areas, suggesting that these species are likely to become invasive species of European grasslands soon.

New Insight Into the Mechanism of Ecological Effects of Artificial Habitats: Elucidating the Relationship Between Protists Associated With Artificial Reefs and Adjacent Seawater

Artificial habitat deployment can restore natural habitats or supplement existing natural habitats. The effect of resource proliferation and protection is obvious. However, few reports have addressed the biological community association between artificial habitats and adjacent environments. Here, Illumina sequencing of 18S rDNA was performed, and the diversity, community structure, and co-occurrence networks of protists in different layers of artificial reefs (ARs) and adjacent seawater (WAR) were described to verify that constructing ARs in Bailong Pearl Bay improves local spatial heterogeneity and functional diversity. In terms of the degree of species interaction, the protist communities were ranked as follows: surface and bottom of WAR &gt; ARs and WAR &gt; different layers of ARs. The α-diversity of protists associated with ARs and WAR decreased with an increase in depth. Protist diversity was greater in WAR than in ARs. β-Diversity analysis revealed significant differences in protist community structure between WAR and ARs (P &lt; 0.05), and the upper layers of ARs and the middle or bottom layers of ARs differed. The key topological features of protist networks showed more positive interspecific interactions in the AR-associated protist community, a higher degree of niche differentiation, and higher complexity and stability. The keystone protists in the bottom seawater layer displayed community functions that were biased toward initial fixation in the ocean carbon cycle. The AR-associated protist community tended to participate in carbon transfer in the food chain and decomposition and utilization of dissolved organic matter (DOM). This study revealed significant differences in protist community structure between ARs and the adjacent environment, and the ecological functions of the key phyla were found to be related. In conclusion, protist communities in WAR may provide food sources for AR-associated heterotrophic protists. A variety of key phyla associated with ARs have biological roles in the carbon pump via their ecological characteristics.

Consistent Grime’s CSR Strategy of Daisy Fleabane Erigeron annuus (L.) Pers. despite Its High Morphological Variability—A Case Study from Zagreb and Medvednica Mt., Croatia

Alongside the direct destruction of natural habitats and changes in land use, invasive species are considered one of the greatest threats to global biodiversity. Daisy fleabane Erigeron annuus (L.) Pers. is among the most widespread invasive plants in Croatia. Invasions of E. annuus may be aided by morphological variability, which this study investigates. The variability of life traits (stem height, fresh and dry leaf mass, length, width and leaf area, specific leaf area, and leaf dry matter content) was examined among 18 locations throughout Zagreb and Medvednica Mt. Overall, 87 plant specimens and 435 leaves were measured and analysed using univariate and multivariate statistics. Viable populations were recorded in diverse habitat types, mostly with marked human impact. We determined Grime’s CR plant life strategies for all, except for two localities with C/CR plant strategies. Two populations with a more pronounced competitive strategy had high leaf dry matter content, with smaller leaves and medium height stems. Significant differences between the localities were found, with the specific leaf area (SLA) and plant height being the most diverse. Despite its high morphological variability, daisy fleabane had a consistent CSR strategy, which likely enables its widespread invasions across variable habitats.

The impact of reduced tillage and distance to field margin on predator functional diversity

Introduction Agricultural intensification results in biodiversity loss through land conversion and management practices which negatively impact arthropods. The abundance and diversity of ground-dwelling predators, e.g. ground beetles (Coleoptera: Carabidae) and spiders (Araneae), are negatively affected by soil disturbances such as tillage. Reducing soil disturbances can potentially conserve arthropod populations in the field and reduce the use of chemical pest controls. The present study investigated the ground-dwelling predatory community using pitfall traps in cereal fields with three different levels of soil disturbance: conventional tillage, reduced tillage and no tillage under Conservation Agriculture management, in 2018 and 2019. Pitfall traps were placed in transects from the field margins. Overall, the activity-density of ground-dwelling predators was higher in fields with minimum soil disturbance and generally declined with increased distance to semi-natural habitats. Functional diversity, expressed by the body size of ground beetles, was also affected by soil disturbances; large ground beetles more consistently occurred in CA, while few or none of the largest ground beetles were found in RT and CT. A higher sample-heterogeneity in less disturbed fields was indicated by a more variable median and higher skewness in the number of predators in those fields. In 2019 only, species diversity was higher along field edges bordering semi-natural habitats when compared to the cropped area. Our results show that reduced tillage supports predator arthropod communities at a local scale: It also bolsters agro-ecosystem resilience by promoting a higher activity-density and by increasing the heterogeneity and functional diversity of ground-dwelling predators. Implications for insect conservation The results obtained in the present study show that soil disturbances significantly influence arthropod abundance and diversity. Conservation of epigeic natural enemies in the agricultural landscape is improved by reducing soil-disturbing events such as tillage.