Smear slide analysis: getting started

by Amy Myrbo

After preparing your smear slides, view them using a petrographic (polarizing light) microscope.  It is nice to have an external light source (such as a fiberoptic or LED illuminator) nearby to apply incident light to see the true color of opaque grains.

Scan around the whole slide at ~100x (typically the 10x objective) to see whether sediment is distributed evenly.  (For instance, larger grains sometimes go to the edges of the wet area.)  Find a representative area or two to zoom in on.

Switch to 400x.  Focus up and down to see particles in different focal planes.  Throughout the analysis, be sure to switch regularly between plane-polarized and cross-polarized light, because some components are difficult or impossible to see in one or the other.


Identifying components in smear slides

Contaminants.  Some components are not meant to be in your slide.  These rogue materials include bubbles in the optical cement, fibers from your clothes, and small particles of the toothpicks used to make slides.  In slides prepared during more permissive times, you may find cigarette ash, which reportedly looks like a zeolite (Kelts 2003).

The prominent circular objects you see, with very high relief (dark edges) are bubbles in the optical cement.  You may also see bubbles filling some microfossils – the heavy dark edges are the clue.

bubbles

bubbles within diatom frustules

a fiber

toothpick shard in plane- and cross-polarized light

Wooden toothpick shards look a lot like muscovite mica.  Avoid this contaminant by using good quality wooden toothpicks that don't shed, or replacing toothpicks with stainless steel or plastic implements.

The good stuff.  In spite of the apparently great variety of materials in a smear slide, 99% of the particles you see belong to one of four groups.  They are:

Organic matter

Diatoms

Siliciclastics

Carbonates

Let’s go through these one by one.

Organic matter

The translucent brown material you see is organic matter – dead tissue.  There is (1) the amorphous brown goo with no structure, which is decomposing algal organic matter, and there is (2) the brown stuff in which you can see cell structure, which is the remains of "higher" (vascular) plants that grew rooted on shore or in the water.  This material is also termed "cuticle."  (There may also be remains of aquatic mosses, which are not vascular but are not amorphous.)  Both may be mixed or encrusted with other subfossil remains, minerals, etc., but their identifying characteristic is the translucent brown color (but see also insect remains and chitin, below).

amorphous algal organic matter

higher plant material showing cell structure

There may also be (3) opaque, or nearly opaque, brown to black particles of irregular shapes.  These are soil organic matter (also called carbonized organic matter).  If the particles are really black (and if incident light shows them to be iridescent), they are charcoal.  Charcoal may have more delicate structure than soil organic matter because it is deposited via air rather than being washed into the lake.  Soil organic matter will usually be associated with other terrestrial materials such as phytoliths and clastic minerals, and may be subangular to subrounded in outline.

charcoal

Observations to make.  You usually can’t identify the plant of origin from material in a smear slide.  What you should do instead is to note the relative abundances of amorphous, vascular, and soil organic matter.  This provides environmental information - for instance, about productivity in the lake vs. material eroded in; or water depth/clarity.

Diatoms

The most eye-catching components of lake sediments are diatoms.  They come in many shapes, but are generally cylindrical (appearing circular or rectangular depending on how they lie on the slide) or elongate.  The cylindrical ones are radially symmetrical, are usually planktonic, and are called centric diatoms.  The elongate ones are bilaterally symmetrical, are usually benthic, and are called pennate diatoms.  These groups are not hard and fast, but it’s a good start.  Diatom remains (frustules, the cell walls) are made of amorphous silica (like opal or glass) and disappear under cross-polarized light because they are isotropic.

an assemblage of freshwater diatoms including planktonic and benthic forms

Observations to make.  Identifying diatoms to genus or species is an expert’s job, and one that can be difficult with a petrographic microscope, at 400x, and with a sample mounted in optical cement.  But even the non-expert can gather some information by observing whether the diatom flora is diverse or only has a few species; whether the diatoms are well preserved, or broken or dissolved; and making some sketches of shapes to compare between slides.  (The simplest type of diatom analysis is to count planktonic vs benthic or centric vs. pennate, which can provide information on water depth and clarity.)  All of these observations can provide environmental information, and will also help you determine whether to bring in a professional diatomist. Much more on diatom identification, taxonomy, and environmental significance can be found at  Diatoms of the US.

Siliciclastics

Cross the nicols and observe the grains that light up.  Rotate the stage to make sure that you are seeing all of them.  Most of are probably gray or white, and some large grains may have dark pink and orange colors. There are also grains with green or brown body color that may mask their birefringence colors.  (For now, ignore the grains that light up brightly in pastel colors.  These are carbonates and are part of the last group, below.) 

Birefringence colors are one of the key characteristics we use to identify minerals using a petrographic microscope. Carbonate minerals have very high birefringence, while silicates typically have moderate to low birefringence. Keep in mind that birefringence is dependent on not only mineralogy but grain size - so thicker grains will have higher birefringence than a thinner grain of the same mineral.  Thus quartz in a thin section (30 um) will appear gray, while a coarse-silt-sized (~60 um) or larger quartz grain in a smear slide will have purple, blue, and dark yellow colors.

The gray and white grains are quartz and feldspar.  Silt-sized grains of these minerals look similar to one another, but if a grain displays a straight edge, it's feldspar (since quartz has conchoidal fracture, and no cleavage).

quartz in plane- and cross-polarized light

feldspar (microcline) in plane- and cross-polarized light

If you are accustomed to looking at thin sections, the birefringence colors of larger quartz grains (>40 μm) may confuse you: at these thicknesses, quartz is at the upper rather than the lower end of first-order colors - red, dark yellow, dark purple, etc.  Contrast these colors with the pastel high-order birefringence colors of carbonates and the vivid medium-order birefringence colors of many heavy minerals.

a large quartz grain in plane- and cross-polarized light

The green or brown (sometimes red) grains are mafic (or ferromagnesian) minerals.  The author's favorite in smear slide is olivine.

olivine (central high-relief grain) in plane- and cross-polarized light

There are also heavy minerals (e.g., epidote, tourmaline, zircon, garnet, rutile, apatite; and opaques such as magnetite, pyrite, marcasite), many of which have a characteristic vivid medium-order birefringence and high relief. 

tourmaline in plane- and cross-polarized light

rutile (high relief twinned crystal) in plane- and cross polarized light

It is not always necessary to identify every silicate clastic grain in lake sediments.  Small lakes in uniform surficial geology will not usually vary over time in their mineralogy (but see below for important textural observations that should be made).  In contrast, in large lakes with, e.g., inlets draining different geologies, significant changes in mineralogy, and thus provenance, can indicate climatic, tectonic, and vegetational changes.  For a primer on identification of silicate minerals in smear slides, see the siliciclastics tutorial.

Observations to make.  Siliciclastic mineralogy is important, but in small lakes perhaps not as important as noting the grain size, sorting, and rounding of the silicate grains as a population.  If your microscope is not calibrated so that you can determine the actual size of objects in the field of view, it’s easy to do so if you have an eyepiece micrometer (reticule) and a stage micrometer or even a transparent ruler.

Get used to the size ranges of clay (below 4 μm or 2 μm, depending on whom you ask), sand (&gt:63 μm), and especially silt (4-63 μm, by far the most common grain size in lakes except large lakes).  It is easy to make a semi-quantitative observation such as “clayey silt” or “silty sand” – which is really all you need in order to make a first-order environmental interpretation.

Guidance on interpreting sorting and roundness is widely available.

Carbonates

Calcite is overwhelmingly the most common carbonate mineral in lake sediments, and indeed the most common authigenic component of lake sediments.  In contrast to the marine system, almost all lacustrine carbonate is inorganically precipitated (though bio-mediated by the changes in pH and carbonate saturation induced by photosynthesis) in lake surface waters.  This authigenic calcite typically appears as regular to corroded rhombs.  (Dissolution or corrosion occurs in lake bottom waters at low pH and low carbonate saturation.)  For more detail on identification and analysis of carbonates, see the carbonate tutorial.

calcite in plane- and cross-polarized light

Aragonite appears as needles or long rice grains, and indicates a high dissolved Mg:Ca ratio.

aragonite in plane- and cross-polarized light

Dolomite, while rare, appears as tight, equant rhombs but overlaps with calcite in appearance and the two phases can be readily confused.

dolomite in plane- and cross-polarized light

  

The myriad iron-manganese-etc carbonates (such as the relatively common siderite and rarer rhodocrosite) are frequently diagenetic (formed post-depositionally) or precipitated in lake bottom waters (because they require reduced Fe and Mn species).  They have been understudied, and are poorly characterized environmentally, despite their exceedingly important role as indicators of anoxia, alkalinity, and overturn.

siderite in plane- and cross-polarized light

rhodocrosite in plane-and cross-polarized light

The main distinguishing feature of carbonate minerals is their high-order birefringence colors.  This is manifested best in large calcite grains as concentric rings of pastel blues and pinks, but as a whole, carbonates look fundamentally different from any silicate mineral.  Thick grains of quartz may show reds and oranges, but these are readily distinguished from the diagnostic colors of carbonates.

Birefringence colors are one of the key characteristics we use to identify minerals using a petrographic microscope. Carbonate minerals have very high birefringence, while silicates typically have moderate to low birefringence. Keep in mind that birefringence is dependent on not only mineralogy but grain size - so thicker grains will have higher birefringence than a thinner grain of the same mineral.  Thus quartz in a thin section (30 um) will appear gray, while a coarse-silt-sized (~60 um) or larger quartz grain in a smear slide will have purple, blue, and dark yellow colors.

We separate carbonates from other minerals because they are a common precipitate in lakes – not just a detrital component – and so they have their own environmental significance.  Detrital carbonates (derived from limestone bedrock or till) may be present; they are typically >50 μm (authigenic carbonates can only grow to about 30 μm before they sink), polycrystalline, and beat up.

detrital calcite grain in plane- and cross-polarized light

The calcifying green alga Phacotus has a calcite lorica, a spherical shell that falls apart in halves when the organism dies.  It is a common component of the sediments in temperate hardwater lakes.  It has a characteristic birefringence pattern that looks like baseball seams, or a pinwheel that turns as you rotate the stage.  If you look closely, there are two distinct forms, which probably represent lorica halves lying concave-up and concave-down.

Phacotus in plane- and cross-polarized light

Observations to make.   Carbonate mineralogy is a good indicator of lake water chemistry and ionic strength, but you have to be at fairly high ionic strength (and high Mg:Ca) to get anything but calcite.  If you only have calcite, there are still important observations:  How large are the grains?  Are they authigenic or detrital?  If both are present, what is the size break between them (e.g., if you wanted to sieve out the detrital calcite, what size mesh would you use?)?  Do grains look nice, even, perhaps rhombohedral (as the first example above), or are they scraggly and corroded?  Do they look polycrystaline and chunky, as is characteristic of shallow-water carbonates (which may be associated with plant matter)?

characteristic shallow-water polycrystalline calcite grain in plane- and cross-polarized light

Other components

Less abundant but environmentally significant sedimentary grains include volcanic glass and diagenetic and biological components.

Volcanic glass is easy to identify in smear slides because it is isotropic. Glass shards may also have distinctive morphological features such as bubbles or broken bubble walls, stretched textures, and scythe-like edges, but isotropy is the diagnostic feature. Devitrifying edges of glass shards, crystalline inclusions, and mineral grains that accompany glass in some tephras may show birefringence. Depending on chemical composition, volcanic glass may be colorless or relatively dark.

volcanic glass in plane- and cross-polarized light

Pyrite, an iron sulfide, forms diagenetically in reducing environments with S and Fe.  It appears as tiny (~1-10 μm) opaque euhedra and larger framboids, and filling in cavities in microfossils.

pyrite euhedra

Vivianite, an iron phosphate, is the only common blue material in smear slides.  (It is white and chalky on the core face when fresh, and oxidizes to bright blue over a few hours.)  It forms diagenetically in reducing environments with P and Fe.  It can indicate rapid burial and/or high P availability.  Phosphorus is effectively recycled in the water column or at the sediment surface under normal conditions (it's frequently a limiting nutrient), but high sedimentation rates can sequester P in the sediments.  Vivianite can form in association with the breakdown of P-rich materials such as animal and plant tissue (bones, seeds, etc.) and can be found as a coating in such objects as well as disseminated in the sediments.

vivianite (blue grains)

Iron oxides and hydroxides can be opaque or non-opaque, and span a range of mineralogies that are not always easily distinguished in smear slide.  Opaque iron oxides, some of which are also classified as heavy minerals, require reflected light to aid in identification.  Non-opaque iron (hydr)oxides include hematite and "limonite," which is actually a mixture of minerals including goethite.

hematite (crystalline) in plane- and cross-polarized light

Chitin is the material comprising the exoskeleton of insects, zooplankton, and other organisms.  It appears in smear slides as transparent colorless to brown sheets in organic shapes (you can recognize body parts such as mandibles and antennae, or see how the curved edges of a plate would fit together with others).  A polymer, it is readily distinguished from similarly-colored plant remains by its absence of internal cell structure.hematite (crystalline) in plane- and cross-polarized light

zooplankton chitin

Phytoliths are intra- or extracellular amorphous silica deposits formed in the tissues of some plants.  (Calcium oxalate phytoliths also exist.)  They have many shapes, but are all isotropic and colorless (unless burned) and often have a purplish hue in plane light.

one of the many shapes of phytoliths (purplish grain, center)

Sponge spicules are also composed of amorphous silica, and look somewhat like diatoms, but much larger - up to about 1000 μm.  Double-ended needles are the most common freshwater form, and the groove running most of the length of the spicule is characteristic.  Like phytoliths, they often appear purplish in plane light.

sponge spicules, both bumpy and smooth

TMI recommends that you keep track of your observations in a systematic way, such as by using one of our smear slide templates.