Ancient environmental DNA reveals shifts in dominant mutualisms during the late Quaternary

Mycorrhizal Symbiosis Increases Plant Phylogenetic Diversity and Regulates Community Assembly in Grasslands

The intricate mechanisms controlling plant diversity and community composition are cornerstone of ecological understanding. Yet, the role of mycorrhizal symbiosis in influencing community composition has often been underestimated. Here, we use extensive species survey data from 1315 grassland sites in China to elucidate the influence of mycorrhizal symbiosis on plant phylogenetic diversity and community assembly. We show that increasing mycorrhizal symbiotic potential leads to greater phylogenetic dispersion within plant communities. Mycorrhizal species predominantly influence deterministic processes, suggesting a role in niche-based community assembly. Conversely, non-mycorrhizal species exert a stronger influence on stochastic processes, highlighting the importance of random events in shaping community structure. These results underscore the crucial but often hidden role of mycorrhizal symbiosis in driving plant community diversity and assembly. This study provides valuable insights into the mechanisms shaping ecological communities and the way for more informed conservation that acknowledges the complex interplay between symbiosis and community dynamics.

The multiscale feedback theory of biodiversity

Plants and their environments engage in feedback loops that not only affect individuals, but also scale up to the ecosystem level. Community-level negative feedback facilitates local diversity, while the ability of plants to engineer ecosystem-wide conditions for their own benefit enhances local dominance. Here, we suggest that local and regional processes influencing diversity are inherently correlated: community-level negative feedback predominates among large species pools formed under historically common conditions; ecosystem-level positive feedback is most apparent in historically restricted habitats. Given enough time and space, evolutionary processes should lead to transitions between systems dominated by positive and negative feedbacks: species-poor systems should become richer due to diversification of dominants and adaptation of subordinates; however, new monodominants may emerge due to migration or new adaptations.

MetaDamage tool: Examining post-mortem damage in sedaDNA on a metagenomic scale

The use of metagenomic datasets to support ancient sedimentary DNA (sedaDNA) for paleoecological reconstruction has been demonstrated to be a powerful tool to understand multi-organism responses to climatic shifts and events. Authentication remains integral to the ancient DNA discipline, and this extends to sedaDNA analysis. Furthermore, distinguishing authentic sedaDNA from contamination or modern material also allows for a better understanding of broader questions in sedaDNA research, such as formation processes, source and catchment, and post-depositional processes. Existing tools for the detection of damage signals are designed for single-taxon input, require a priori organism specification, and require a significant number of input sequences to establish a signal. It is therefore often difficult to identify an established cytosine deamination rate consistent with ancient DNA across a sediment sample. In this study, we present MetaDamage, a tool that examines cytosine deamination on a metagenomic (all organisms) scale for multiple previously undetermined taxa and can produce a damage profile based on a few hundred reads. We outline the development and testing of the MetaDamage tool using both authentic sedaDNA sequences and simulated data to demonstrate the resolution in which MetaDamage can identify deamination levels consistent with the presence of ancient DNA. The MetaDamage tool offers a method for the initial assessment of the presence of sedaDNA and a better understanding of key questions of preservation for paleoecological reconstruction.

Postglacial species arrival and diversity buildup of northern ecosystems took millennia

What drives ecosystem buildup, diversity, and stability? We assess species arrival and ecosystem changes across 16 millennia by combining regional-scale plant sedimentary ancient DNA from Fennoscandia with near-complete DNA and trait databases. We show that postglacial arrival time varies within and between plant growth forms. Further, arrival times were mainly predicted by adaptation to temperature, disturbance, and light. Major break points in ecological trait diversity were seen between 13.9 and 10.8 calibrated thousand years before the present (cal ka BP), as well as break point in functional diversity at 12.0 cal ka BP, shifting from a state of ecosystem buildup to a state where most habitat types and biotic ecosystem components were in place. Trait and functional diversity stabilized around 8 cal ka BP, after which both remained stable, although changes in climate took place and species inflow continued. Our ecosystem reconstruction indicates a millennial-scale time phase of formation to reach stable and resilient levels of diversity and functioning.

The application and potential non-conservatism of stable isotopes in organic matter source tracing

Organic matter (OM) tracing is critical for understanding the processes of soil redistribution and global carbon cycling. It effectively supports ecological management and global climate change prediction. Stable isotopes are generally more source-specific compared with other tracers and identify OM sources with a higher level of accuracy. Nevertheless, stable isotopes may be enriched or depleted by physical and biochemical processes such as selective migration of particles and OM mineralization in transport and sedimentary environments, making it difficult to establish links between the source and sink regions. Literature on OM source identification tends to assume a direct link between stable isotope sources and sinks, ignoring the non-conservatism of stable isotopes. There is further literature on understanding and modeling the processes that link the sources to sinks in terms of the non-conservatism of stable isotopes. The disagreement in response to the non-conservatism lies in the lack of comprehensive understanding of stable isotope fingerprinting systems and non-conservatism. The development of stable isotope fingerprinting technology is full of challenges. This review outlines the applicability of stable isotope tracers, identification mechanisms, and associated quantitative models, intending to improve the stable isotope fingerprinting system. We highlight the non-conservatism of stable isotopes in space and time caused by physical and biochemical processes. Additionally, a decision tree is established to determine the quantitative tools, evaluation indicators, and procedures related to non-conservatism. This decision tree clarifies the process from non-conservatism detection to threshold determination of statistical quantification, which can guide the end-users to better apply stable isotope to trace OM sources.

Factors Affecting the Natural Regeneration of the Larix principis-rupprechtii Mayr Plantations: Evidence from the Composition and Co-Occurrence Network Structure of Soil Bacterial Communities

Bacterial communities living in the soil can affect forests natural regeneration, but the effects of their composition and network inference on regeneration of Larix principis-rupprechtii Mayr plantations remain largely elusive. Therefore, the redundancy analysis and structure equations modeling of affecting elements for the regeneration of L. principis-rupprechtii plots including the diversity, composition and network structure of soil bacteria, topographic factors, light factors, and soil physicochemical properties have been conducted. It was found that the increased modularity of the soil bacterial community co-occurrence network and the enrichment of metabolic pathway bacteria had a significant positive effect on the successful regeneration (total effect of 0.84). The complexity of the soil bacterial community gradually decreased with the increase of stand regeneration, and the composition and structure of the flora became simpler (with standard path coefficients: −0.70). In addition, altitude also had a positive effect on regeneration with a total effect of 0.39. Soil nutrients had significantly negative effects on regeneration with total effects of −0.87. Soil bacterial communities may mediate the effects of soil nutrients, altitude, litter thickness, and herbaceous diversity on regeneration in L. principis-rupprechtii plantations. The results provide a great contribution to our understanding of regeneration-soil bacterial community interactions and the basis and important data for sustainable management of L. principis-rupprechtii plantations in the Lvliang Mountains located in northern China.

Environmental DNA analysis as an emerging non-destructive method for plant biodiversity monitoring: a review

Environmental DNA (eDNA) analysis has recently transformed and modernized biodiversity monitoring. The accurate detection, and to some extent quantification, of organisms (individuals/populations/communities) in environmental samples is galvanizing eDNA as a successful cost and time-efficient biomonitoring technique. Currently, eDNA's application to plants remains more limited in implementation and scope compared to animals and microorganisms. This review evaluates the development of eDNA-based methods for (vascular) plants, comparing its performance and power of detection with that of traditional methods, to critically evaluate and advise best-practices needed to innovate plant biomonitoring. Recent advancements, standardization and field applications of eDNA-based methods have provided enough scope to utilize it in conservation biology for numerous organisms. Despite our review demonstrating only 13% of all eDNA studies focus on plant taxa to date, eDNA has considerable environmental DNA has considerable potential for plants, where successful detection of invasive, endangered and rare species, and community-level interpretations have provided proof-of-concept. Monitoring methods using eDNA were found to be equal or more effective than traditional methods; however, species detection increased when both methods were coupled. Additionally, eDNA methods were found to be effective in studying species interactions, community dynamics and even effects of anthropogenic pressure. Currently, elimination of potential obstacles (e.g. lack of relevant DNA reference libraries for plants) and the development of user-friendly protocols would greatly contribute to comprehensive eDNA-based plant monitoring programs. This is particularly needed in the data-depauperate tropics and for some plant groups (e.g., Bryophytes and Pteridophytes). We further advocate to coupling traditional methods with eDNA approaches, as the former is often cheaper and methodologically more straightforward, while the latter offers non-destructive approaches with increased discrimination ability. Furthermore, to make a global platform for eDNA, governmental and academic-industrial collaborations are essential to make eDNA surveys a broadly adopted and implemented, rapid, cost-effective and non-invasive plant monitoring approach.

Global taxonomic and phylogenetic assembly of AM fungi

Arbuscular mycorrhizal (AM) fungi are a ubiquitous group of plant symbionts, yet processes underlying their global assembly - in particular the roles of dispersal limitation and historical drivers - remain poorly understood. Because earlier studies have reported niche conservatism in AM fungi, we hypothesized that variation in taxonomic community composition (i.e., unweighted by taxon relatedness) should resemble variation in phylogenetic community composition (i.e., weighted by taxon relatedness) which reflects ancestral adaptations to historical habitat gradients. Because of the presumed strong dispersal ability of AM fungi, we also anticipated that the large-scale structure of AM fungal communities would track environmental conditions without regional discontinuity. We used recently published AM fungal sequence data (small-subunit ribosomal RNA gene) from soil samples collected worldwide to reconstruct global patterns in taxonomic and phylogenetic community variation. The taxonomic structure of AM fungal communities was primarily driven by habitat conditions, with limited regional differentiation, and there were two well-supported clusters of communities - occurring in cold and warm conditions. Phylogenetic structure was driven by the same factors, though all relationships were markedly weaker. This suggests that niche conservatism with respect to habitat associations is weakly expressed in AM fungal communities. We conclude that the composition of AM fungal communities tracks major climatic and edaphic gradients, with the effects of dispersal limitation and historic factors considerably less apparent than those of climate and soil.

A Standardized Approach for Shotgun Metagenomic Analysis of Ancient Dental Calculus

Ancient dental calculus provides a challenging, yet unparalleled, opportunity to reconstruct ancient oral microbial communities and trace the origins of modern microbiota-associated diseases. Metagenomic analysis of ancient dental calculus using high-throughput DNA sequencing has proven itself as an effective method to accurately reconstruct microorganisms that once lived in the mouths of ancient humans. Here, we provide the strategy, methodologies, and approaches used to establish an ancient dental calculus project, from project conception, community engagement, sampling, extracting DNA, and preparing shotgun metagenomic DNA libraries for sequencing on an Illumina platform. We also discuss techniques to minimize background or contaminant DNA by monitoring and reducing contamination in calculus data sets, utilizing appropriate protective gear, and employing the use of sample decontamination strategies. In this methodology chapter, we hope to promote transparency in the ancient dental calculus research field and encourage collaboration across the ancient DNA research community.

The Future of DNA Barcoding: Reflections from Early Career Researchers

Over the last two decades, the use of DNA barcodes has transformed our ability to identify and assess life on our planet. Both strengths and weaknesses of the method have been exemplified through thousands of peer-reviewed scientific articles. Given the novel sequencing approaches, currently capable of generating millions of reads at low cost, we reflect on the questions: What will the future bring for DNA barcoding? Will identification of species using short, standardized fragments of DNA stand the test of time? We present reflected opinions of early career biodiversity researchers in the form of a SWOT analysis and discuss answers to these questions.

Overkill, glacial history, and the extinction of North America's Ice Age megafauna

The end of the Pleistocene in North America saw the extinction of 38 genera of mostly large mammals. As their disappearance seemingly coincided with the arrival of people in the Americas, their extinction is often attributed to human overkill, notwithstanding a dearth of archaeological evidence of human predation. Moreover, this period saw the extinction of other species, along with significant changes in many surviving taxa, suggesting a broader cause, notably, the ecological upheaval that occurred as Earth shifted from a glacial to an interglacial climate. But, overkill advocates ask, if extinctions were due to climate changes, why did these large mammals survive previous glacial-interglacial transitions, only to vanish at the one when human hunters were present? This question rests on two assumptions: that previous glacial-interglacial transitions were similar to the end of the Pleistocene, and that the large mammal genera survived unchanged over multiple such cycles. Neither is demonstrably correct. Resolving the cause of large mammal extinctions requires greater knowledge of individual species' histories and their adaptive tolerances, a fuller understanding of how past climatic and ecological changes impacted those animals and their biotic communities, and what changes occurred at the Pleistocene-Holocene boundary that might have led to those genera going extinct at that time. Then we will be able to ascertain whether the sole ecologically significant difference between previous glacial-interglacial transitions and the very last one was a human presence.

Plant functional groups associate with distinct arbuscular mycorrhizal fungal communities

The benefits of the arbuscular mycorrhizal (AM) symbiosis between plants and fungi are modulated by the functional characteristics of both partners. However, it is unknown to what extent functionally distinct groups of plants naturally associate with different AM fungi. We reanalysed 14 high-throughput sequencing data sets describing AM fungal communities associating with plant individuals (2427) belonging to 297 species. We examined how root-associating AM fungal communities varied between plants with different growth forms, photosynthetic pathways, CSR (competitor, stress-tolerator, ruderal) strategies, mycorrhizal statuses and N-fixing statuses. AM fungal community composition differed in relation to all studied plant functional groups. Grasses, C₄ and nonruderal plants were characterised by high AM fungal alpha diversity, while C₄ , ruderal and obligately mycorrhizal plants were characterised by high beta diversity. The phylogenetic diversity of AM fungi, a potential surrogate for functional diversity, was higher among forbs than other plant growth forms. Putatively ruderal (previously cultured) AM fungi were disproportionately associated with forbs and ruderal plants. There was phylogenetic correlation among AM fungi in the degree of association with different plant growth forms and photosynthetic pathways. Associated AM fungal communities constitute an important component of plant ecological strategies. Functionally different plants associate with distinct AM fungal communities, linking mycorrhizal associations with functional diversity in ecosystems.

Conservation Genomics in a Changing Arctic

Although logistically challenging to study, the Arctic is a bellwether for global change and is becoming a model for questions pertinent to the persistence of biodiversity. Disruption of Arctic ecosystems is accelerating, with impacts ranging from mixing of biotic communities to individual behavioral responses. Understanding these changes is crucial for conservation and sustainable economic development. Genomic approaches are providing transformative insights into biotic responses to environmental change, but have seen limited application in the Arctic due to a series of limitations. To meet the promise of genome analyses, we urge rigorous development of biorepositories from high latitudes to provide essential libraries to improve the conservation, monitoring, and management of Arctic ecosystems through genomic approaches.

Conceptual differences lead to divergent trait estimates in empirical and taxonomic approaches to plant mycorrhizal trait assignment

Empirical and taxonomic approaches are the two main methods used to assign plant mycorrhizal traits to species lists. While the empirical approach uses only available empirical information, the taxonomic approach extrapolates certain core information about plant mycorrhizal types and statuses to related species. Despite recent claims that the taxonomic approach is now almost definitive, with little benefit to be gained from further empirical data collection, it has not been thoroughly compared with the empirical approach. Using the most complete available plant mycorrhizal trait information for Europe and both assignment approaches, we calculate the proportion of species for each trait, and model environmental drivers of trait distribution across the continent. We found large degrees of mismatch between approaches, with consequences for biogeographical interpretation, among facultatively mycorrhizal (FM; 91% of species mismatched), non-mycorrhizal (NM; 45%), and to a lesser extent arbuscular mycorrhizal (AM; 16%) plant species. This can partly be attributed to the taxonomic precision of the taxonomic approach and the use of different AM, NM, and FM concepts. Our results showed that the extrapolations of the taxonomic approach do not consistently match with empirical information and indicate that more empirical data are needed, in particular for FM, NM, and AM plant species. Clarifying certain concepts underlying mycorrhizal traits and empirically describing NM, AM, and FM species within plant families can greatly improve our understanding of the biogeography of mycorrhizal symbiosis.