Agar-Block Microcosms for Controlled Plant Tissue Decomposition by Aerobic Fungi

Summary

This video demonstrates a controlled environment approach to study degradation of lignocellulosic plant tissues by aerobic fungi. The ability to control nutrient sources and moisture is a key advantage of agar-block microcosms, but the approach often yields mixed success. We address critical pitfalls to yield reproducible, low-variability results.

Abstract

The two principal methods for studying fungal biodegradation of lignocellulosic plant tissues were developed for wood preservative testing (soil-block; agar-block). It is well-accepted that soil-block microcosms yield higher decay rates, fewer moisture issues, lower variability among studies, and higher thresholds of preservative toxicity. Soil-block testing is thus the more utilized technique and has been standardized by American Society for Testing and Materials (ASTM) (method D 1413-07). The soil-block design has drawbacks, however, using locally-variable soil sources and in limiting the control of nutrients external (exogenous) to the decaying tissues. These drawbacks have emerged as a problem in applying this method to other, increasingly popular research aims. These modern aims include degrading lignocellulosics for bioenergy research, testing bioremediation of co-metabolized toxics, evaluating oxidative mechanisms, and tracking translocated elements along hyphal networks. Soil-blocks do not lend enough control in these applications. A refined agar-block approach is necessary.

Here, we use the brown rot wood-degrading fungus Serpula lacrymans to degrade wood in agar-block microcosms, using deep Petri dishes with low-calcium agar. We test the role of exogenous gypsum on decay in a time-series, to demonstrate the utility and expected variability. Blocks from a single board rip (longitudinal cut) are conditioned, weighed, autoclaved, and introduced aseptically atop plastic mesh. Fungal inoculations are at each block face, with exogenous gypsum added at interfaces. Harvests are aseptic until the final destructive harvest. These microcosms are designed to avoid block contact with agar or Petri dish walls. Condensation is minimized during plate pours and during incubation. Finally, inoculum/gypsum/wood spacing is minimized but without allowing contact. These less technical aspects of agar-block design are also the most common causes of failure and the key source of variability among studies. Video publication is therefore useful in this case, and we demonstrate low-variability, high-quality results.

Protocol

This protocol applies to woody and non-woody substrates, as outlined, as well as to oven- or air-dried material. Read through the protocol first, however, before set-up. There are several points raised that may apply to your study, and these points (underlined) require planning. Also, note that there are two published agar-block methods that are occasionally used, one the British Standard 838 and another following an International Research Group on Wood Protection (IRG-WP) paper submitted by Bravery (1978). Our resembles method 838, with modifications primarily in the microcosm design and the control of the agar medium, but again, both approaches are often avoided due....

Discussion

Using our agar-block set-up (Figure 1) Serpula lacrymans grew in direct contact with the gypsum surfaces and into wood blocks (Figure 2), leading to more than 60% weight loss in the control brown-rotted pine blocks (Figure 3). This easily satisfies the ASTM standard goal of >50% decay, and the average coefficient of variation (C_V) in decay at was 0.055 at week 16. This data is published in Schilling⁷. Again, other fungi will require longer incubation in agar-block than in soil-block. Fo.......

Materials

List of materials used in this article

Name	Company	Catalog Number	Comments
Petri dishes	Nalge Nunc international	4014	25 x 150 mm
Agar, Type A	Sigma-Aldrich	A4550
Ammonium nitrate, NH4NO3	Millinckrodt	3436-12
Potassium phosphate, KH2PO4	JT Baker	3246-01
Magnesium sulfate 7-hydrate, MgSO4•7H2O	Sigma-Aldrich	230391
D-(+)-Glucose	Sigma-Aldrich	G8270	Dextrose
Boric acid, H3BO4	Mallinckrodt Baker Inc.	2549-04
Zinc sulfate 7-hydrate, ZnSO4•7H2O	Mallinckrodt Baker Inc.	8880-12
Manganous chloride 4-hydrate, MnCl2•4H2O	JT Baker	2540-04
Copper(II) sulfate 5-hydrate, CuSO4•5H2O	Sigma-Aldrich	209198
Ammonium heptamolybdate 4-hydrate, (NH4)6Mo7O24•4H2O	Sigma-Aldrich	431346
Calcium chloride dihydrate, CaCl2•2H2O	Mallinckrodt Baker Inc.	4160-12
Sodium chloride, NaCl	Mallinckrodt Baker Inc.	7581-12
Ferrous sulfate 7-hydrate, FeSO4•7H2O	Mallinckrodt Baker Inc.	5056-12
Pipet-aid	Drummond Scientific	4-000-110	Cordless EtOH the surface
10 ml sterile polystyrene pipette	BD Biosciences	357551
Gutter Guard	Thermwell Products Co.	VX620	Pre-scrubbed with soap Hardware store
Calcium sulfate hemihydrate, CaSO4•0.5H2O	Acros Organics	385355000
#4 cork borer	Boekel Scientific	1601
Parafilm "M"	Pechiney Plastic Packaging	PM-996