Phytoliths in Paleoecology: Analytical Considerations, Current Use, and Future Directions

A rapid and simple method for the extraction of biogenic silica (BSi) in phytolith-poor sediments and soils

Phytoliths can be used to reconstruct human-nature dynamics over the long term (from decennial to centennial and millennial time scales) and may capture activities that cannot be reconstructed through other proxies. Phytoliths consist of fossil biogenic silica (BSi), formed in plant organs and then released into the soil with plant decay. When working in environmental contexts where the phytolith signal is highly diluted, as is the case in environments with a long history of land use, animal-plant interactions and open woody environments, the extraction of phytoliths remains a challenge. To address this issue, we developed an efficient method for the extraction of biogenic silica (BSi) from sediments and soils of contexts characterised by the long-term human and animal presence and disturbance, such as remnants of old agroforestry systems. The method we developed has a number of advantages, including: •An easy and time-efficient methodology to perform (with an overall processing time of 1.5/2 days for a batch of 16 samples)•An extraction method free from dangerous chemicals•A method amenable to non-experts without a prior background in lab extraction procedures.

Silicon: A valuable soil element for improving plant growth and CO2 sequestration

BACKGROUND

Silicon (Si), the second most abundant and quasi-essential soil element, is locked as a recalcitrant silicate mineral in the Earth's crust. The physical abundance of silicates can play an essential role in increasing plant productivity. Plants store Si as biogenic silica (phytoliths), which is mobilized through a chemical weathering process in the soil.

AIM OF REVIEW

Although Si is a critical element for plant growth, there is still a considerable need to understand its dissolution, uptake, and translocation in agroecosystems. Here, we show recent progress in understanding the interactome of Si, CO2, the microbiome, and soil chemistry, which can sustainably govern silicate dissolution and cycling in agriculture.

KEY SCIENTIFIC CONCEPTS OF THIS REVIEW

Si cycling is directly related to carbon cycling, and the resulting climate stability can be enhanced by negative feedback between atmospheric CO2 and the silicate uptake process. Improved Si mobilization in the rhizosphere by the presence of reactive elements (for example, Ca, Na, Al, Zn, and Fe) and Si uptake through genetic transporters in plants are crucial to achieving the dual objectives of (i) enhancing crop productivity and (ii) abiotic stress tolerance. Furthermore, the microbiome is a symbiotic partner of plants. Bacterial and fungal microbiomes can solubilize silicate minerals through intriguingly complex bioweathering mechanisms by producing beneficial metabolites and enzymes. However, the interaction of Si with CO2 and the microbiome's function in mobilization have been understudied. This review shows that enhancing our understanding of Si, CO2, the microbiome, and soil chemistry can help in sustainable crop production during climatic stress events.

Phytolith particulate matter and its potential human and environmental effects

Particulate matter from both natural and anthropogenic sources is known to affect air quality and human health. However, the abundance and varied composition of the suspended particulate matter make it difficult to locate the precise precursors for some of these atmospheric pollutants. Plants deposit appreciable quantities of microscopic biogenic silica in and/or between their cells, known as phytoliths, which get released into the soil surface after the death and decomposition of plants. Dust storms from exposed terrains, forest fires, and stubble burning disperse these phytoliths into the atmosphere. Their durability, chemical composition, and diverse morphology prompt us to view phytoliths as a possible particulate matter that could impact air quality, climate, and human health. Estimating the phytolith particulate matter, its toxicity, and environmental impacts will help take effective and targeted policies for improving air quality and decreasing health risks.

Oldest evidence of abundant C4 grasses and habitat heterogeneity in eastern Africa

The assembly of Africa's iconic C₄ grassland ecosystems is central to evolutionary interpretations of many mammal lineages, including hominins. C₄ grasses are thought to have become ecologically dominant in Africa only after 10 million years ago (Ma). However, paleobotanical records older than 10 Ma are sparse, limiting assessment of the timing and nature of C₄ biomass expansion. This study uses a multiproxy design to document vegetation structure from nine Early Miocene mammal site complexes across eastern Africa. Results demonstrate that between ~21 and 16 Ma, C₄ grasses were locally abundant, contributing to heterogeneous habitats ranging from forests to wooded grasslands. These data push back the oldest evidence of C₄ grass-dominated habitats in Africa-and globally-by more than 10 million years, calling for revised paleoecological interpretations of mammalian evolution.

The evolution of hominoid locomotor versatility: Evidence from Moroto, a 21 Ma site in Uganda

Living hominoids are distinguished by upright torsos and versatile locomotion. It is hypothesized that these features evolved for feeding on fruit from terminal branches in forests. To investigate the evolutionary context of hominoid adaptive origins, we analyzed multiple paleoenvironmental proxies in conjunction with hominoid fossils from the Moroto II site in Uganda. The data indicate seasonally dry woodlands with the earliest evidence of abundant C₄ grasses in Africa based on a confirmed age of 21 million years ago (Ma). We demonstrate that the leaf-eating hominoid Morotopithecus consumed water-stressed vegetation, and postcrania from the site indicate ape-like locomotor adaptations. These findings suggest that the origin of hominoid locomotor versatility is associated with foraging on leaves in heterogeneous, open woodlands rather than forests.

A morphological guide of neotropical freshwater sponge spicules for paleolimnological studies

Freshwater sponges (Porifera: Spongillida) are sessile invertebrates with skeletons composed of siliceous elements termed spicules. Sponge spicules (megascleres, microscleres, and gemmuloscleres) are characterized by widely varying sizes and shapes. These spicules are well-preserved in lacustrine, wetland, and riverine sediments and hold significant ecological and limnological information that can be applied as diagnostic tools in reconstructions of Quaternary environments. However, problems with taxonomy and the absence of systematic guidelines and standards of identification represent major challenges to utilizing freshwater sponges as a paleo-proxy. Here, we present a well-illustrated extraction protocol and morphological guide to the Neotropical freshwater sponge fauna. This guide is intended to introduce researchers and students to the study of freshwater sponges and their use as a diagnostic tool in paleoecology and paleolimnology.

Middle to late Holocene plant cover variation in relation to climate, fire, and human activity in the Songnen grasslands of northeastern China

INTRODUCTION

For future vegetation projections and conservation planning in grassland ecosystems, accurate estimates of past plant cover changes in grassland composition and their responses to the various driving factors are essential. This study quantitatively reconstructs the past regional plant cover in the Songnen grasslands (northeastern China) and explores the relative importance of climate, fire, and human activity on vegetation dynamics.

METHODS

For this purpose, the Regional Estimates of Vegetation Abundance from Large Sites (REVEALS) model is applied to three pollen records from two areas, two in the center of the Songnen grasslands and one located in an area marginal to the grasslands.

RESULTS

Results from the most reliable REVEALS scenarios show that from the mid-Holocene, steppe (mean cover 40.6%) and dry steppe (mean cover 54.2%) alternately dominated the central part of the Songnen grasslands while the marginal grasslands were mainly characterized by alternating broadleaved forests (mean cover 26.3%), coniferous forests (mean cover 41.9%) and dry steppes (mean cover 30.1%).

DISCUSSION

By comparing the plant cover results with previous published regional climate, fire and human activity records, the results show that long term vegetation dynamics were mainly driven by East Asia Summer Monsoon (EASM) and the related precipitation variations, but was also affected by fire frequency and human activity. Moreover, vegetation evolution was sensitive to abrupt cooling events including the 4.2 ka BP and stacked ice-rafted debris (IRD) events; the change from steppe to dry steppe, for example, was driven by these abrupt climate changes. Fire events can alter the original vegetation stability allowing the vegetation to respond rapidly to climate changes while human activity merely has limited influence on vegetation changes.

The origin and evolution of open habitats in North America inferred by Bayesian deep learning models

Some of the most extensive terrestrial biomes today consist of open vegetation, including temperate grasslands and tropical savannas. These biomes originated relatively recently in Earth’s history, likely replacing forested habitats in the second half of the Cenozoic. However, the timing of their origination and expansion remains disputed. Here, we present a Bayesian deep learning model that utilizes information from fossil evidence, geologic models, and paleoclimatic proxies to reconstruct paleovegetation, placing the emergence of open habitats in North America at around 23 million years ago. By the time of the onset of the Quaternary glacial cycles, open habitats were covering more than 30% of North America and were expanding at peak rates, to eventually become the most prominent natural vegetation type today. Our entirely data-driven approach demonstrates how deep learning can harness unexplored signals from complex data sets to provide insights into the evolution of Earth’s biomes in time and space.

The expansion timing and dynamics of open vegetation are disputed. Here, the authors present a model of paleovegetation changes in North America, showing open vegetation beginning around 23 million years ago and accelerating at 5 million years ago to become the most prominent natural vegetation type in North America today.

Phylogenetic, ecological and intraindividual variability patterns in grass phytolith shape

BACKGROUND AND AIMS

Grass silica short cell (GSSC) phytoliths appear to be the most reliable source of fossil evidence for tracking the evolutionary history and paleoecology of grasses. In recent years, modern techniques that quantitatively assess phytolith shape variation have widened opportunities for the classification of grass fossil phytoliths. However, phylogenetic, ecological and intraindividual variability patterns in phytolith shape remain largely unexplored.

METHODS

The full range of intraindividual phytolith shape variation [3650 two-dimensional (2-D) outlines] from 73 extant grass species, 48 genera, 18 tribes and eight subfamilies (particularly Pooideae) was analysed using geometric morphometric analysis based on semi-landmarks spanning phytolith outlines.

KEY RESULTS

The 2-D phytolith shape is mainly driven by deep-time diversification of grass subfamilies. There is distinct phytolith shape variation in early-diverging lineages of Pooideae (Meliceae, Stipeae). The amount of intraindividual variation in phytolith shape varies among species, resulting in a remarkable pattern across grass phylogeny.

CONCLUSIONS

The phylogenetic pattern in phytolith shape was successfully revealed by applying geometric morphometrics to 2-D phytolith shape outlines, strengthening the potential of phytoliths to track the evolutionary history and paleoecology of grasses. Geometric morphometrics of 2-D phytolith shape is an excellent tool for analysis requiring large numbers of phytolith outlines, making it useful for quantitative palaeoecological reconstruction.

Phytolith Palaeoenvironments at Mumba Rock Shelter

The rock shelter site of Mumba in northern Tanzania plays a pivotal role in the overall study of the late Pleistocene archaeology of East Africa with an emphasis on the Middle to Later Stone Age transition. We used phytolith analysis to reconstruct general plant habitat physiognomy around the site from the onset of the late Pleistocene to recent times, tallying 4246 individual phytoliths from 19 archaeological samples. Statistical analysis explored phytolith richness, diversity, dominance, and evenness, along with principal components to compare phytolith distributions over the site’s sequence with known plant habitats today. Generally, the phytolith record of Mumba signifies paleoenvironments with analogs in the Somalia – Masai bushland and grassland, as well as Zambezian woodlands.

Inter- and intraspecific variation in grass phytolith shape and size: a geometric morphometrics perspective

BACKGROUND AND AIMS

The relative contributions of inter- and intraspecific variation to phytolith shape and size have only been investigated in a limited number of studies. However, a detailed understanding of phytolith variation patterns among populations or even within a single plant specimen is of key importance for the correct taxonomic identification of grass taxa in fossil samples and for the reconstruction of vegetation and environmental conditions in the past. In this study, we used geometric morphometric analysis for the quantification of different sources of phytolith shape and size variation.

METHODS

We used landmark-based geometric morphometric methods for the analysis of phytolith shapes in two extant grass species (Brachypodium pinnatum and B. sylvaticum). For each species, 1200 phytoliths were analysed from 12 leaves originating from six plants growing in three populations. Phytolith shape and size data were subjected to multivariate Procrustes analysis of variance (ANOVA), multivariate regression, principal component analysis and linear discriminant analysis.

KEY RESULTS

Interspecific variation largely outweighed intraspecific variation with respect to phytolith shape. Individual phytolith shapes were classified with 83 % accuracy into their respective species. Conversely, variation in phytolith shapes within species but among populations, possibly related to environmental heterogeneity, was comparatively low.

CONCLUSIONS

Our results imply that phytolith shape relatively closely corresponds to the taxonomic identity of closely related grass species. Moreover, our methodological approach, applied here in phytolith analysis for the first time, enabled the quantification and separation of variation that is not related to species discrimination. Our findings strengthen the role of grass phytoliths in the reconstruction of past vegetation dynamics.

3D shape analysis of grass silica short cell phytoliths: a new method for fossil classification and analysis of shape evolution

Fossil grass silica short cell phytoliths (GSSCP) have been used to reconstruct the biogeography of Poaceae, untangle crop domestication history and detect past vegetation shifts. These inferences depend on accurately identifying the clade to which the fossils belong. Patterns of GSSCP shape and size variation across the family have not been established and current classification methods are subjective or based on a 2D view that ignores important 3D shape variation. Focusing on Poaceae subfamilies Anomochlooideae, Pharoideae, Pueliodieae, Bambusoideae and Oryzoideae, we observed in situ GSSCP to establish their orientation and imaged isolated GSSCP using confocal microscopy to produce 3D models. 3D geometric morphometrics was used to analyze GSSCP shape and size. Classification models were applied to GSSCP from Eocene sediments from Nebraska, USA, and Anatolia, Turkey. There were significant shape differences between nearly all recognized GSSCP morphotypes and between clades with shared morphotypes. Most of the Eocene GSSCP were classified as woody bamboos with some distinctive Nebraska GSSCP classified as herbaceous bamboos. 3D morphometrics hold great promise for GSSCP classification. It accounts for the complete GSSCP shape, automates size measurements and accommodates the complete range of morphotypes within a single analytical framework.

Soil and plant phytoliths from the Acacia-Commiphora mosaics at Oldupai Gorge (Tanzania)

This article studies soil and plant phytoliths from the Eastern Serengeti Plains, specifically the Acacia-Commiphora mosaics from Oldupai Gorge, Tanzania, as present-day analogue for the environment that was contemporaneous with the emergence of the genus Homo. We investigate whether phytolith assemblages from recent soil surfaces reflect plant community structure and composition with fidelity. The materials included 35 topsoil samples and 29 plant species (20 genera, 15 families). Phytoliths were extracted from both soil and botanical samples. Quantification aimed at discovering relationships amongst the soil and plant phytoliths relative distributions through Chi-square independence tests, establishing the statistical significance of the relationship between categorical variables within the two populations. Soil assemblages form a spectrum, or cohort of co-ocurring phytolith classes, that will allow identifying environments similar to those in the Acacia-Commiphora ecozone in the fossil record.

International Code for Phytolith Nomenclature (ICPN) 2.0

BACKGROUND

Opal phytoliths (microscopic silica bodies produced in and between the cells of many plants) are a very resilient, often preserved type of plant microfossil. With the exponentially growing number of phytolith studies, standardization of phytolith morphotype names and description is essential. As a first effort in standardization, the International Code for Phytolith Nomenclature 1.0 was published by the ICPN Working Group in Annals of Botany in 2005. A decade of use of the code has prompted the need to revise, update, expand and improve it.

SCOPE

ICPN 2.0 formulates the principles recommended for naming and describing phytolith morphotypes. According to these principles, it presents the revised names, diagnosis, images and drawings of the morphotypes that were included in ICPN 1.0, plus three others. These 19 morphotypes are those most commonly encountered in phytolith assemblages from modern and fossil soils, sediments and archaeological deposits. An illustrated glossary of common terms for description is also provided.

Plant carbon assimilation rates in atmospheric CO2 reconstructions

Fossil plant gas-exchange-based CO₂ reconstructions use carbon (C) assimilation rates of extant plant species as substitutes for assimilation rates of fossil plants. However, assumptions in model species adoption can lead to systematic error propagation. We used a dataset of c. 2500 extant species to investigate the role of phylogenetic relatedness and ecology in determining C assimilation, an essential variable in gas-exchange-based CO₂ models. We evaluated the effect on random and systematic error propagation in atmospheric CO₂ caused by adopting different model species. Phylogenetic relatedness, growth form, and solar exposure are important predictors of C assimilation rate. CO₂ reconstructions that apply C assimilation rates from modern species based solely on phylogenetic relatedness to fossil species can result in CO₂ estimates that are systematically biased by a factor of > 2. C assimilation rates used in CO₂ reconstructions should be determined by averaging assimilation rates of modern plant species that are (1) in the same family and (2) have a similar habit and habitat as the fossil plant. In addition, systematic bias potential and random error propagation are greatly reduced when CO₂ is reconstructed from multiple fossil plant species with different modern relatives at the same site.