Sina M. Adl

The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists

Abstract. This revision of the classification of unicellular eukaryotes updates that of Levine et al. (1980) for the protozoa and expands it to include other protists. Whereas the previous revision was primarily to incorporate the results of ultrastructural studies, this revision incorporates results from both ultrastructural research since 1980 and molecular phylogenetic studies. We propose a scheme that is based on nameless ranked systematics. The vocabulary of the taxonomy is updated, particularly to clarify the naming of groups that have been repositioned. We recognize six clusters of eukaryotes that may represent the basic groupings similar to traditional “kingdoms.” The multicellular lineages emerged from within monophyletic protist lineages: animals and fungi from Opisthokonta, plants from Archaeplastida, and brown algae from Stramenopiles.

How many species are there on Earth and in the ocean

The diversity of life is one of the most striking aspects of our planet; hence knowing how many species inhabit Earth is among the most fundamental questions in science. Yet the answer to this question remains enigmatic, as efforts to sample the worlds biodiversity to date have been limited and thus have precluded direct quantification of global species richness, and because indirect estimates rely on assumptions that have proven highly controversial. Here we show that the higher taxonomic classification of species (i.e., the assignment of species to phylum, class, order, family, and genus) follows a consistent and predictable pattern from which the total number of species in a taxonomic group can be estimated. This approach was validated against well-known taxa, and when applied to all domains of life, it predicts ∼8.7 million (±1.3 million SE) eukaryotic species globally, of which ∼2.2 million (±0.18 million SE) are marine. In spite of 250 years of taxonomic classification and over 1.2 million species already catalogued in a central database, our results suggest that some 86% of existing species on Earth and 91% of species in the ocean still await description. Renewed interest in further exploration and taxonomy is required if this significant gap in our knowledge of life on Earth is to be closed.

The revised classification of eukaryotes.

This revision of the classification of eukaryotes, which updates that of Adl et al. [J. Eukaryot. Microbiol. 52 (2005) 399], retains an emphasis on the protists and incorporates changes since 2005 that have resolved nodes and branches in phylogenetic trees. Whereas the previous revision was successful in re‐introducing name stability to the classification, this revision provides a classification for lineages that were then still unresolved. The supergroups have withstood phylogenetic hypothesis testing with some modifications, but despite some progress, problematic nodes at the base of the eukaryotic tree still remain to be statistically resolved. Looking forward, subsequent transformations to our understanding of the diversity of life will be from the discovery of novel lineages in previously under‐sampled areas and from environmental genomic information.

Diversity, Nomenclature, and Taxonomy of Protists

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Relative effects of macroinvertebrates and habitat on the chemistry of litter during decomposition

Summary During the decomposition of terrestrial leaf litter, the concentrations of lignin, tannin, cellulose, hemicellulose, nitrogen, and carbon are known to change. These chemical changes have been associated with subsequent colonization and activity of decomposer flora and fauna. Here, we report that chemical changes in litter during the first twelve months of decomposition are affected by macroinvertebrate activity. Moreover, chemical changes are associated most closely with the activities of invertebrate predators. Using litter bags that either excluded (fine mesh) or allowed access by (coarse mesh) macroinvertebrates, we followed the concentrations of lignin, tannin, cellulose, hemicellulose, nitrogen, and carbon in the litter of Liriodendron tulipifera, Quercus prinus and Rhododendron maximum in a North Carolina forest ecosystem. We also compared chemical changes in these litters at a riparian site and an upland site within the forest. The exclusion of macroinvertebrates decreased concentrations of nitrogen and total phenolics in the litter of L. tulipifera, increased concentrations of cellulose and condensed tannin in Q. prinus litter, and increased the concentrations of condensed tannin in R. maximum litter in the riparian zone. Although fine mesh bags excluded most macroinvertebrates, the greatest effects of exclusion were upon ants and spiders, not macroinvertebrate decomposers. Our data therefore suggest that predator-mediated changes in the decomposer communities were responsible for observed shifts in litter chemistry. Predator effects on litter chemistry were likely mediated by their interactions with fungivorous and bacterivorous fauna. For example, Collembola populations were 34% higher in litter bags from which macroinvertebrates were excluded. Litter chemistries also differed between the riparian and upland sites. For both L. tulipifera and R. maximum, effects of habitat were limited to higher concentrations of condensed tannin in the upland site. In contrast, habitat effects upon the litter chemistry of Q. prinus were pervasive. Specifically, Q. prinus litter in the upland habitat exhibited slower increases in lignin, more stable concentrations of cellulose, slower increases in hemicellulose, higher concentrations of total phenolics, and higher concentrations of hydrolysable tannins than did litter in the riparian habitat. Overall, our data provide the first evidence that predators in the litter of deciduous forests can influence the chemistry of litter during the decomposition process.

Protozoan Pulses Unveil Their Pivotal Position Within the Soil Food Web

Protozoa are one of the most abundant groups of bacterivores within the soil and are responsible for mineralisation of bacterial biomass, having a large impact on C and N cycling. Little is known of their contribution to soil nutrient transfers or the identity of their consumers. Here, for the first time indigenous flagellates and ciliates, enriched to 83 atom% for 13C and 10 atom% for 15N, were introduced to soil cores from two different land managements, grassland and woodland with the same soil type, to trace the flow of protozoan C and N through the soil food web. Nematodes, Collembola, earthworms and insect larvae obtained the greatest amounts of C and N of protozoan origin, either through direct consumption or uptake of biomass post-cell death. Our results show that changes in management, affect the functioning of the soil food web and the utilisation of protozoa as a food source.

Dynamics of soil protozoa using a direct count method

We adapted a direct count method for obtaining counts of active protozoa that was not overly time consuming. Soil samples from an agricultural field were examined at 1- to 3-day intervals three times through the year. The three sampling periods represented different weather conditions. At each sampling event, fresh soil samples were extracted upon return to the laboratory for protozoa. These were enumerated at the microscope without prior culture, in soil–water suspension dilutions. We describe a procedure that allowed all samples to be processed in a few hours. Our results suggest there is good reproducibility and agreement between samples collected on the same day. Our data resolve differences between days as soil conditions changed slowly with drying or wetting. This procedure is suitable for describing species active at the time of sampling. Unlike the ‘most probable number’ procedure that relies on cultivable species, it is less prone to enumerating excysting individuals, and it provides better resolution between sampling dates, with a relatively low number of samples.

Using stable isotopes to differentiate trophic feeding channels within soil food webs.

The soil is probably the most diverse habitat there is, with organisms ranging in sizes from less than 1 μm to several metres in length. However, it is increasingly evident that we know little about the interactions occurring between these organisms, the functions that they perform as individual species, or together within their different feeding guilds. These interactions between groups of organisms and physical and chemical processes shape the soil as a habitat and influence the nature of the soil food web with consequences for the above‐ground vegetation and food web. Protists are known as one of the most abundant groups of bacterivores within the soil; however, they are also consumers of a number of other food sources. Even though they are responsible for a large proportion of the mineralisation of bacterial biomass and have a large impact on the C and N cycles within the soil they are regularly overlooked when investigating the complete soil food web. Recently, stable isotopes have been used to determine trophic interactions and here we describe how this technique has been used to highlight linkages between protists and the soil food web.

Protist-like inclusions in amber, as evidenced by Charentes amber

The mid-Cretaceous amber of France contains thousands of protist-like inclusions similar in shape to some ciliates, flagellates and amoebae. The sheer abundance of these inclusions and their size variation within a single amber piece are not concordant with true fossil protists. French amber is coniferous in origin, which generally does not preserve well protists without cell walls. Thus, it would be surprising if French Cretaceous amber had preserved millions of protists. Here, we present a survey of the protist-like inclusions from French amber and attempt to elucidate their origins. Diverse Cretaceous ambers (from Spain, Germany and Lebanon), also derived from conifer resins, contain thousands of protist-like inclusions. In contrast, Tertiary ambers and modern resins are poor in protist-like fossils. This suggests these inclusions originated from early Cretaceous plant resins, probably secreted with the resin by trees that did not survive after the Cretaceous (such as the Cheirolepidiaceae). A review of the recent literature on amber microfossils indicates several protist-like inclusions that are unlikely to have a biological origin have already been described as real fossil protists. This is problematic in that it will bias our understanding of protist evolution.

Effects of Altered Temperature and Precipitation on Desert Protozoa Associated with Biological Soil Crusts

ABSTRACT. Biological soil crusts are diverse assemblages of bacteria, cyanobacteria, algae, fungi, lichens, and mosses that cover much of arid land soils. The objective of this study was to quantify protozoa associated with biological soil crusts and test the response of protozoa to increased temperature and precipitation as is predicted by some global climate models. Protozoa were more abundant when associated with cyanobacteria/lichen crusts than with cyanobacteria crusts alone. Amoebae, flagellates, and ciliates originating from the Colorado Plateau desert (cool desert, primarily winter precipitation) declined 50‐, 10‐, and 100‐fold, respectively, when moved in field mesocosms to the Chihuahuan Desert (hot desert, primarily summer rain). However, this was not observed in protozoa collected from the Chihuahuan Desert and moved to the Sonoran desert (hot desert, also summer rain, but warmer than Chihuahuan Desert). Protozoa in culture began to encyst at 37°C. Cysts survived the upper end of daily temperatures (37–55°C), and could be stimulated to excyst if temperatures were reduced to 15°C or lower. Results from this study suggest that cool desert protozoa are influenced negatively by increased summer precipitation during excessive summer temperatures, and that desert protozoa may be adapted to a specific deserts temperature and precipitation regime.