soil-microscopy – Heather Comina

Garden amendments – some myths and tips

In some of my earlier posts on healthy soil and composts I have alluded to the use of compost extracts, teas and other garden amendments but what are they and when are they useful?

When I first started on my path to regenerating my soil and growing healthier plants I found the literature on the topic of garden amendments quite confusing. There seemed to be so many options of things to make or buy and conflicting information about their potential benefits. Over time and quite a bit of research and experimentation I have come to realise a few things which I would like to share with you here. For the sake of simplicity I will refer to compost extracts, teas and other preparations collectively as amendments.

Before I go into any detail on which amendments are useful and which are not, I feel it useful to discuss briefly why we might want to use them at all – do we need anything more than good compost? When we have healthy soils and are only needing to add compost to replenish soil nutrients used up by the previous crop then I would argue we probably don’t need extra amendments, but since most of us or a journey towards healthy soil there are situations in which amendments can give a valuable boost to our plants and soils.

Many soils are deficient in key minerals which plants need for healthy growth and, critically, they lack a healthy population of soil food web biology which is essential for establishing a healthy plant microbiome. In the early years of soil regeneration the judicious use of appropriate amendments can help us to produce healthier plants which in turn, when we compost their residues, can lead to the generation of healthier soils in subsequent seasons. Thus, amendments are a useful way of rapidly addressing chemical nutrient and plant biology imbalances allowing us to kick start our soil regeneration.

Ahead of discussing what I would term useful amendments I would like to briefly mention some amendments that are not useful, or even desirable (and why).

Undesirable amendments – typically high in chemical nutrients but possessing undesirable biology.

Liquids which leach out from the bottom of compost piles or worm bins. I see a lot of references to this and I would warn against their use. Whilst they may contain useful plant nutrients they are typically unpleasant smelling which means they have been formed under anaerobic conditions in which many pathogenic bacteria thrive and thus are not a source of desirable plant biology. [As a side note – if you are keen on making high quality worm compost (which does not produce any leachate) then you might want to check out Rhonda Sherman’s guide]
Compost left to steep in water for a few days, unaerated and then filtered and used to water plants – this is sometimes referred to as compost tea. Again the same issues as for compost leachate apply – anaerobic conditions foster the growth of undesirable microbes. There are better ways to make compost teas, we will come back to this later.
Preparations of plant matter which are left in water for a number of days or weeks. This seems to be a common way of making “fertiliser” preparations from plants such as nettles or for decomposing roots of plants like couch grass or bind weed. Whilst these methods are effective at extracting valuable nutrients they again suffer from the same problem of introducing undesirable biology which is signified by the extremely unpleasant smell produced by such concoctions! Again there are better ways to utilise such plants as nutrient sources, I will touch on these later on.

Like me, I expect you have used some of the above amendments. Why wouldn’t you – you see recommendations for them everywhere! The reasoning most people offer for their use is that they work. After a fashion they do, mostly because of the high chemical nutrient levels they possess. But the effects are often short lived and the risks of introducing undesirable (pathogenic, disease causing) microbes outweighs any benefits to their use in my opinion.

So what should we do instead? The answer depends on what the soil or plants need – what are they deficient in? This could be either chemical nutrients (i.e. key minerals) or biology (i.e. imbalanced soil food web populations). You can determine what is missing by observing your plants/soils or by directly testing them. Lets take each case in turn.

Nutrient deficiencies can be apparent from observing the leaves and shoots of your plants which will show fairly characteristic problems if for example there are low levels of nitrogen, phosphorous, iron, magnesium, calcium etc. The lack of other key minerals such as sulfur, boron, manganese etc. can be harder to spot but equally important.

To better understand your soil chemistry it is a good idea to send off a sample to be tested, there are some labs that will test samples from small growers and gardeners at a very reasonable price. Once you have an idea of any imbalances in your soil nutrient/mineral levels then you can look to address this by adding appropriate amendments many of which you can prepare yourself from cheap and readily available sources.

I don’t want to go into a lot of detail on the preparation of nutrient amendments here – this could be an article all of its own. I will just describe a couple that I have used to good effect and point you towards further sources of information.

Both nettles and comfrey are a good source of mineral nutrients – see the table below for a summary. You can of course add these to your compost pile to enrich the compost that you make but if you want a more immediate source of mineral supplements to address deficiencies in your plants and soil then you can make an extract called fermented plant juice (FPJ) which will be shelf stable for up to a year and (if made correctly) will not smell unpleasant.

The secret to making FPJ is to use a lot of sugar which acts to extract moisture from the plant material and dehydrate any microbes so that they go dormant rather than multiplying. The result is a rich, dark liquid which smells strongly of the plant you extracted; in the case of nettle and comfrey is a distinctive rich earthy smell. You can find out how to make FPJ (and other related Korean Natural Farming – KNF – approaches) by clicking on the links here – Nigel Palmer FPJ prep – https://www.biomei.solutions/resources

I tend to make a fresh batch of FPJ in the late spring using either nettles from the end of my garden or the comfrey which I cultivate next to my compost heaps. Once its ready to use it can be diluted (approx. 500-1000 fold) in rain water and added to plants either as a soil soak or sprayed onto leaves to give a more immediate mineral boost. Its always a good idea to do a sniff check before you use it, especially if you’ve stored it for a while. If it smells musty, rotten or chemical (like alcohol or nail polish remover) then don’t use it at will not do your plants any good – you can recycle it into your compost heap and make a new batch.

I have used these simple extracts to good effect for the past couple of years particularly to address issues with mineral deficiencies in my fruit bushes and to help young plants build resilience towards attack from aphids and other insects. As my initial soil test results (see earlier) identified a slight sulfur deficiency I have also found nettle FPJ to be a good supplement to feed my brassicas and alliums with.

Home made Nettle FPJ made from garden nettles

Soil biology imbalances are not as complex to address as they might seem. After all if you are making good quality compost under aerobic conditions you are already on the road to doing this. So what biological amendments can you readily make and when would you use them? This is a huge topic so I will focus on the approaches I have been using thus far and point you to further options at the end of our discussion.

Again the best way to know what your soil is missing is to analyse some samples, in this case using a microscope. Thanks to excellent tuition from Eddie at Rhizophyllia I learned to do this myself, at least to a level which gives me a qualitative guide. If you feel this is beyond you, then again there are places which will test the soil biology for you.

If soil analysis is not an option for you then fear not! There are some simple signs of what could be missing based on things you can observe about your soil and plants, I will allude to these in the discussion below.

Compost Extract – biology amendment with several potential uses.

Add to mulches to aid their break down – symptom to be addressed – so called constipated soils which have a lot of undecomposed organic matter on or near the surface. These tend to be high in bacteria but not much other biology and thus can’t break down organic matter in the soil very effectively.
Inoculate seeds or the roots of transplants – symptom to be addressed – seedlings and young plants are weak with poor root systems and vulnerable to attack from pests (e.g slugs, aphids)

Compost extracts are very simple to prepare and use. All you need is some good quality compost and some rain water, a small bucket, funnel and some filter mesh (typically I use 100 micron brewing mesh). Ideally the compost has been analysed to ensure that it contains a good level of soil food web biology but if you cant do that then use your nose; if it smells in any way unpleasant then don’t use it!

This season I chose to use some of the hot compost that I prepared in the spring as it was rich in soil food web members – see my earlier compost diary post on this topic.

Here is a quick recipe which provides about a litre of compost extract.

Place 1 litre of rainwater in a small bucket
Add approx. 100g of good quality compost
Stir gently and allow to stand for about 30 mins then stir again
Filter through mesh into a clean container
Dilute roughly 10 fold before use (e.g. 1 litre of extract in 10 litres of rain water to be applied using a watering can)

Summing up key points

Amendments can be useful to address deficiencies in poor soils at the start of your regenerative journey.
Pay attention to both mineral nutrients and soil biology – your plants need both
Be careful about using amendments that may come from anaerobic processes – don’t use it if it smells bad!

The final class of amendment which deserves a mention is Actively Aerated Compost Tea which can be used as a soil soak and/or foliar spray to further enhance the health of soils and plants. Making good quality aerated composted teas is something of an art and I have yet to fully get to grips with approach. I plan to do some more in-depth experiments in the coming season and will be sure to share my results in future posts. Until then – Happy Growing!

Compost Diary – the evolution of a hot compost pile

Early in the spring I was beginning to run short of home made compost. At the start of May I decided to take advantage of the first flush of grass and comfrey growing at the end of my garden along with the left over mulched leaves that I had cleared from over-wintered beds to make some “Hot Compost“. This composting method is a fantastic way to rapidly access a source of compost which is both rich in nutrients and bursting with soil microbes, ideal for feeding hungry brassica crops and preparing extracts (what I term protist soup) to give plants a regular boost throughout the growing season.

Making hot compost is something of an art. You need a fairly large quantity (at least a cubic metre) of balanced inputs. Roughly a third brown, a third green and a third manure. I discussed compost inputs in some detail in my previous post – The Art of composting; in this case I used dried leaves as the browns, grass cuttings as the greens and a mixture of chopped comfrey, rabbit manure and coffee grounds as the manure components. You also need a fair amount of water (not chlorinated) to ensure the moisture level of the pile is around 80%.

Compost Inputs – from left to right – brown leaves; green cut grass; rabbit manure mixed with coffee grounds and chopped comfrey

The other thing you need is plenty of human energy! The pile needs to be created in one session, building up alternate layers of brown, green, manure, watering as you go. It then needs to be turned every few days to control the temperature, maintain good oxygenation and to ensure that all of the pile is well mixed and exposed to the higher temperatures at the centre. Overall a pretty good workout!

To enable easy turning I constructed the pile inside a wire mesh cage. The inputs were layered in until I had a completed cylinder of roughly 1 cubic metre. I then covered the whole pile with a canvas bag to keep out light and moisture in. The bag and wire cage could be easily removed to allow ready access to the pile for turning – simple.

Stages of construction – from left to right – wire cage; completed layered pile; covered pile

Compared to other composting methods, hot composting is pretty quick, taking just a few weeks to yield a usable compost but how do you know when its ready to use?

One of the ways is to monitor the temperature of the pile using a compost thermometer [See Box 1]. A well made pile heats up pretty quickly the initiation phase typically takes a couple of days. In my case the pile reached 45C in less than a day and by day 3 was already at 65C and needed to be turned to stop it overheating. This hot phase of higher than 40C can last a few days. After 9 days my pile had started to drop below this level and at 16 days was consistently around 25C, finally cooling to 20C by day 37 and beyond.

Box 1 – temperature profile

There are three distinct temperature phases of the composting process – Mesophilic, Thermophilic and Maturation. The length of time the pile spends in each of the phases depends on its size and the type of inputs used.

Mesophilic – composting is driven by organisms which thrive between 20-40C, typically bacteria, some fungi and larger organisms such as protists and nematodes.

Thermophilic – the activity of the organisms in the mesophilic phase creates heat which drives the temperature above 40C. A new set of organisms which thrive in higher temperatures (40-65C) now takes over and the mesophilic organisms die off or go dormant. At these temperatures pathogenic bacteria and any plant seeds are killed off.

Maturation – as the thermophilic organisms rapidly consume the easy to digest nutrients in the compost the temperature begins to cool again. Once the threshold of 40C is reached the dormant mesophilic organisms start to takeover again. Over time the population of soil food web members increases and the slower job of breaking down the harder to digest compost ingredients begins.

The temperature profile of my hot compost pile is shown in the chart below.

Temperature profile of compost pile over the 51 day period

For more detailed information about the stages of the composting process click here.

You can also see visual changes in the compost pile over time. The size of the pile gradually reduces to about a third of the original size and the contents become more and more compost-like in appearance as the plant matter breaks down and the individual inputs become less distinct.

As a general rule of thumb it is recommended to wait for 16 days for the pile to cool and then allow a further week or two before using the compost which at this point will be very fresh and high in nitrogen – ideal for using on hungry crops like brassicas.

But I was curious – at what point would my compost be suitable to use for making an extract (protist soup) and when would it be suitable to use on my beds to feed my brassicas? How was the soil biology profile changing over time?

This is where soil microscopy comes into its own. By taking samples at various points during the lifetime of my compost pile and analysing them under the microscope I was able to get a sense of how the soil food web (SFW) was evolving. For more details on the soil food web see my previous post – Secrets of Healthy Soil.

The detailed results of the microscopy analysis are presented in Box 2. However, there are some key points which I found quite insightful and want to share with you here.

The analysis at day 9, when the hot phase was just coming to an end, showed very high levels of bacteria. This is to be expected as it is mainly bacterial activity that drives the heating of the pile. There were also lots of actinomycetes strands (a type of filamentous bacteria) but only a few protists (mainly flagellates) and no nematodes, this too is not surprising as they don’t like the heat. Fast forward to day 16, now the profile looks quite different. Bacterial numbers are still quite high but we also see nematodes, principally bacterial feeders. The protist levels have also increased with growing numbers of amoeba present.

Day 9 microscopy images at 400x – (a) filaments of Actinomycetes; (b) amoeba and encysted flagellates in a sea of bacteria

Day 16 microscopy images at 100x – (a) nematode; (b) several amoeba

By day 30 the optimal balance of soil food web members appears to have been reached. The nematode population was beginning to evolve further with the presence of larger predatory nematodes as well as the regular bacterial feeders. The protist population was also very vibrant with an array of different types and sizes of amoeba. In addition there were some signs of fungal life with a few fine filaments beginning to emerge from spores. In the final analysis I conducted on day 51, the picture was broadly similar but the nematode and bacteria numbers were showing signs of decreasing as the compost moved into a maturing phase.

Day 30 microscopy images – (a) fungal thread sprouting from spore and amoeba; (b) predatory nematode; (c) amoeba and encysted flagellates; (d) large naked amoeba

Day 51 microscopy images – (a) large amoeba; (b) pair of amoeba; (c) fungal thread

So did the microscopy analysis answer my question – when was the compost ready to use either on my beds or to make protist soup?

Based on the results I would say around day 30 was the optimal point to start using the compost – when the soil food web population was high and well balanced. This ties in nicely with the temperature profile when the pile was pretty much back at around 20C. Visually the compost also looked like compost, it felt and smelled like compost too. Gratifyingly my observations were also in line with the rule of thumb guidance mentioned earlier.

Box 2 – Soil Food Web analysis

Evolution of Soil Food Web population over time

Nematode count – number per drop of sample
Fungal fragment count – average number per field of view at 100x magnification
Beneficial Protist (amoeba, flagellate) count – average number per field of view at 400x magnification
Ciliate count – average number per field of view at 400x magnification
Bacteria count – estimated number of billions in 1g of compost

This semi-quantitative assessment of soil food web (SFW) populations was carried out according to the following protocol:

A sample of hot compost was taken from the middle of the pile during the turning process. 5g of compost was diluted with 50ml of distilled water (1:10 dilution) and shaken gently. After leaving the debris to settle, a drop of the liquid was taken and placed on a microscope slide. Three drops were analysed for each compost sample.

At 40x magnification the number of nematodes on the whole slide was counted.

At 100x magnification the average number of fungal fragments per field of view (FOV) was estimated by counting the fragments in 10 randomly selected fields.

At 400x magnification the average number of protists (amoeba, flagellates and ciliates) per FOV was estimated by counting the number of each observed in 10 randomly selected fields.

To estimate the number of bacteria present a 1ml sample of the initial 1:10 dilution liquid was further diluted to make up 10ml (overall 100 fold dilution). A drop of this sample was placed on a cell counting slide and the number of bacteria present in each of a series of 10 randomly selected 50 micron squares was counted. These values were then used to calculate an estimate of the number of bacteria present in a 1g sample of the compost.

As a reference point the SFW population of a typical mature compost is as follows [data source – Regenerative Soil Microscopy, Matt Powers, p.181]

Bacteria – 4-10 billion per g of compost
Nematodes – 3-7 per drop (beneficial types not root feeders)
Fungi – average of 1-5 fungal strands per FOV at 100x
Beneficial protists – average of 3-12 per FOV at 400x
Ciliates – less than 3-5 per drop

Was all the effort worth it? I am pleased to say my brassicas certainly seemed to like it. I was also able to use the compost to make several batches of protist soup which I applied to my crops every 3-4 weeks across the growing season. Qualitatively the crops look healthier, what I have harvested thus far tastes fantastic. We will have to wait until my end of season soil analysis to get a sense of how effective the application of protist soup has been. I will share this, along with more details on making and using protist soup and related compost teas in my next instalment of the Compost Diary – until then happy growing!

Celebrating Permaculture

The Permaculture movement focusses on nurturing each other and the planet, creating a resilient future together. In that vein the UK Permaculture Association has recently launched its Permaculture Digest, comprising a range of articles and wisdom sharing nuggets written by the members, for the members.

Permaculture Ethics – Earth Care, People Care, Fair Share.
Courtesy of https://permacultureprinciples.com/ethics/

I am excited to have one of my articles “Healthy Soil Secrets” included in the first edition! Click here for a related post on my blog.

Healthy Soil Secrets – Microscope Images of Soil Food Web organisms

If you want to learn more about Permaculture and what the members are up to then head over to the Permaculture Website. There is so much on offer, from training courses, publications, networking and regular events – something for everyone.

Becoming a member is easy. If you would like to join the growing Permaculture family then simply click here.

Growing Better – New Video on Protists available

The second video in my series on Soil Microscopy is now available on the videos page. The theme is Protists (sometimes called Protozoa). There are three main types of Protist which form part of the Soil Food Web family; these are Amoeba, Flagellates and Ciliates. They are much smaller than the nematodes, if you have a good eye you can spot them at 100 fold magnification but they are best viewed at 400 fold magnification (or higher).

I have tried to capture the Protists in their various forms (testate, encysted and naked) to give you a sense of what you might expect to see under the microscope.

Hopefully you find the video a useful guide for your own exploration of soil ecosystems – Enjoy!

Growing Better – New Resources

I’m excited to share with you a couple of new resources that I am compiling to supplement the Growing Better theme.

The first resource is a new gallery page where I am uploading images from my soil microscopy studies. If you ever wondered what common Soil Food Web members look like then hopefully these images will help you.

The second resource is a set of short videos which provide further perspective on some of the more mobile Soil Food Web fauna. I’ve started with a quick overview on nematodes which are perhaps the easiest things to spot when looking under the microscope even at low magnification.

I will gradually be adding to these resources as I explore more soil and compost samples over the coming months. Hopefully you will find them useful in your own exploration of soil ecosystems.