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Soil Science for Gardeners: Working with Nature to Build Soil Health

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Build healthy soil and grow better plants

Healthy soil means thriving plants. Yet untangling the soil food web and optimizing your soil health is beyond most gardeners, many of whom lack an in-depth knowledge of the soil ecosystem.

Soil Science for Gardeners is an accessible, science-based guide to understanding soil fertility and, in particular, the rhizosphere - the thin layer of liquid and soil surrounding plant roots, so vital to plant health.

Robert Pavlis, a gardener for over four decades, debunks common soil myths, explores the rhizosphere, and provides a personalized soil fertility improvement program in this three-part popular science guidebook. Coverage includes:


Soil biology and chemistry and how plants and soil interact
Common soil health problems, including analyzing soil's fertility and plant nutrients
The creation of a personalized plan for improving your soil fertility, including setting priorities and goals in a cost-effective, realistic time frame.
Creating the optimal conditions for nature to do the heavy lifting of building soil fertility
Written for the home gardener, market gardener, and micro-farmer, Soil Science for Gardeners is packed with information to help you grow thriving plants.

224 pages, Paperback

Published April 7, 2020

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About the author

Robert Pavlis

12 books8 followers

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Displaying 1 - 29 of 29 reviews
Profile Image for Lynne.
65 reviews3 followers
March 11, 2023
Definitely a mixed bag! Along with many pearls of wisdom that are rarely available to gardeners, this author also makes some glaring misstatements. And while his information is purported to be science-based, Pavlis fails to use footnotes or citations, which does not impart confidence.

At times one wonders whether some simple editing would have improved the book. He refers to the eastern US as wet, and the western US as dry. Does he know something the rest of us don't?

More to the point, he states flatly that soil is not alive. Perhaps this can be attributed to a matter of perspective or interpretation, but the general consensus is that the soil is a living ecosystem... more than the sum of its parts. Excluded from his definition are critical components of the soil (living and dead organisms) and processes that sustain the soil. The definition of soil has evolved over the last 150 years, and Pavlis seems to throw his hat in with some of the oldest of these (https://www.sciencedirect.com/science...).

There are some good insights and explanations in this book, but I caution against relying on his every word. It's always advantageous to get other authoritative opinions.
81 reviews5 followers
September 22, 2020
I recommend this book to all gardeners who have hesitated to open a soil science text for fear of dry incomprehensible overloads of numbers. Robert Pavlis explains how your garden grows, and dashes cold water on false myths that may have been wasting your time and limiting your success for years! He leads us to a better understanding, including on a microscopic level, of soil biology, chemistry, physics, geology and ecology and to a place of wonder and curiosity at the everyday functioning of crops and soils.
This new comprehension can lead us to do right by our plants and our gardens, leading to healthier plants and higher yields. Robert writes in plain language, as a gardener with over 45 years of experience. He is the author of those Garden Myths books you might have seen. Perhaps, like me, you paid them little attention, thinking your own knowledge was fact-based. Even so, like me, you might find you had been holding onto some anti-facts (mine was that I believed compost is acidic – not so!). This book aims to have us understand real soil and make real improvements, via a Soil Health Action Plan at the end of the book.
The three sections of the book are Understanding Soil, Solving Soil Problems, and A Personalized Plan for Healthy Soil. A satisfying, logical sequence. Read the sections in the order presented! Robert says it’s very easy to grow plants if you understand the soil which anchors them, feeds them and provides the air and water they need to survive. With a solid understanding of what’s going on, you won’t need to memorize rules.
The 2016 definition of soil, by the Soil Science Academy of America is “Soil is the top layer of the Earth’s surface that generally consists of loose rock and mineral particles mixed with dead organic matter.” A rather bland underselling of what soil accomplishes. Here comes myth-bust #1: “Soil is not alive. It does not need to eat or breathe.” “The whole idea that soil is a living organism that requires similar attention to animals is completely false and leads to many poor recommendations for managing soil.” No, don’t give up here! It’s not the soil but the ecosystem of the soil and all the living organisms in and on it that holds the life. The ecosystem contains life, but is not itself alive.
Air and water are critical for good plant growth, about 25% of each. A simple, startling truth. The sand, silt and clay we might worry about make up another 45%, and 5% organic matter might fill out the total. A large tree can remove up to 100 gallons (400 liters) of water a day, discharging most of it into the air as water vapor. As the water leaves the soil, air is pulled in to fill the spaces. Roots pull the oxygen in, day and night, to convert sugars into energy. Were you also lead to believe that plants photosynthesized by day and respired only by night?
Did you know (I hadn’t thought about it) that “soil pH” is really an average of the pH of the water in the soil, and a spot with organic matter and lots of bacterial activity will have a very different pH from a spot with less organic matter? The rhizosphere (the area right around a plant’s roots) can have a very different pH from the soil solution further away. Plants can grow in alkaline soil because their roots are actually growing in acidic conditions. The nitrogen-fixing bacteria on legume roots cause the plant to release hydrogen ions, making the rhizosphere more acidic. To some extent, our efforts to change the soil pH can be undone by our crops and weeds! A soil property called buffer capacity lets the soil absorb materials at different pH and maintain its same level. Peat moss is acidic, but it does not acidify alkaline soil. The soil in the rhizosphere can be 2 pH units different from the soil around. This is usually written about in rather magical terms, but here it is in plain language.
Roots grow just fine where there is enough phosphorus. Adding more at transplanting doesn’t help, and can hinder. Visual plant symptoms can predict possible deficiencies, but are not a reliable diagnosis. Purple leaves may indicate phosphorus deficiency or cold temperatures, high light intensity, pest damage or lack of water. Or a nitrogen shortage reducing the plant’s ability to absorb phosphorus. There’s much that we don’t know!
Pay attention to the Cation Exchange Capacity – the measure of the soil’s ability to hold cations – because many plant nutrients are cations. You can increase the CEC by increasing the clay content, increasing the OM or increasing the pH. Read more in this book.
Have you ever thought about the “free” nitrogen from legume root nodules? Rethink of it as “homegrown” or “solar” rather than simply magic and free, because the leguminous plant may use up to 20% of the sugars produced during photosynthesis, to feed the bacteria.
Don’t justify your adherence to organic gardening by falsely claiming that synthetic fertilizers kill bacteria. Bacteria feed on both synthetic and organic fertilizers. This book challenges us to find the factual basis for choosing to grow organically, making us stronger advocates.
The bacteria chapter is followed by a chapter on fungi. Fungal spores are everywhere, even the Antarctic. Fungi are crucial for cleaning up plant litter on the soil surface. They grow above-ground hyphae which can penetrate dry leaves or wood chips and move the nutrients deep into the soil. Bacteria can’t tackle such tough stuff! 150 species of fungi capture and digest nematodes.
Why is organic matter important? This chapter explores the chemical and biological effects of organic matter on soil. Soil contains three forms of organic carbon: the living (15%), the dead and the very dead (stable humus and charcoal). Increasing the level of organic matter in the soil can increase aggregation, improve water infiltration (reducing runoff), increase aeration, increase water-holding capacity, improve tilth of clay soils, reduce crusting, and improve the size and distribution of the pore spaces. Those are just the physical effects. It will also increase the cation exchange capacity, increase the availability of nitrogen, boron, molybdenum, phosphorus and sulfur, and increase the microbial activity and diversity.
Often we think about adding partially decomposed OM such as compost and manure. We should face the reality that compost tends to have low levels of nutrients (maybe 1:1:1). The big value of these is in providing food for microbes, short-lived beings that provide a constant supply of fresh OM, multiplying its value. Partially decomposed compost takes about five years to finish decomposing, during which time it slowly releases nutrients. This gradual steady supply is what crops need. The humus left at the end is a complex molecular mixture of carbon, hydrogen and oxygen, resistant to further decay.
The initial effect of adding fresh OM (not composted OM) is an explosion of microbial reproduction, feeding and death. The microbes use nitrogen, which can cause plants to suffer a shortage. It takes time for a new balance to be achieved, providing adequate N for the plants. The needs for the N can encourage gardeners to add so much compost that the P level is too high, which can bring death to mycorrhizal fungi, leading to roots driving deeper to access their own P from the soil directly. We have very high soil P, a result of misunderstanding soil test limits. I have worried about it, then read more and stopped worrying. Soil P is pretty stable. If you are not leaching P into a waterway, it just stays in your soil until a plant need it. We switched to using less compost and more cover crops where we could. We were already using a lot of cover crops – it’s not like we were slouches in that department! After more time, I settled on accepting our situation, and as the plants show no sign of P-caused problems and our soil is bursting with earthworms, it doesn’t affect us much.
I mentioned at the beginning that I learned that finished compost is alkaline, not acidic. In the initial composting stage, acidity happens. Then fungi thrive, and decompose the tough lignin and cellulose, causing the pH to rise and bacteria to take over. Compost-making has lots of myths! Poorly understood science makes them grow, I suppose. Bokashi composting, for example (more of a fermentation than a composting process) is based on the idea that fermented material decomposes faster, although it’s unclear if this is really true. “The best method of composting is the one that you do and continue to do because you like doing it. Any form of composting is better than taking yard waste to the curb.”
The Rhizosphere chapter is fascinating! Root exudates can restrict the growth of competing roots, attract microbes into symbiotic relationships, Change the chemical and physical properties of the soil solution and the soil, and make nutrients more available. Bacteria make explosive population growth as they feed on exudates. Then their predators, nematodes and protozoa, join the party. The soil water around the roots becomes a nutrient soup. By photosynthesis, the plants produce the attractive exudates that the soil food web turns into plant nutrients right where the roots can efficiently hoover them up. Plants are active in seeking nutrients, not passive recipients. Not to say they have knowledge, or think and plan. It’s a matter of chemical reactions controlled by enzymes with the capacity to change their activity based on the presence or absence of chemical triggers. Let’s marvel at the reality! We don’t need fairy stories!
The second section of the book, Solving Soil Problems, starts with identifying the problems, and works through techniques affecting the soil, chemical and microbe issues, increasing organic matter and structural problems. We are not feeding plants, we are replacing missing nutrients in the soil, so they can take the nutrients they need. The solution will depend on your soil, so a “tomato fertilizer” is not going to be what tomatoes need in every soil. If you plan to top up the missing nutrients, get a soil test to learn what those are. But if you plan to apply manure or compost everywhere as your only amendment, your money is wasted on a soil test. If you add compost every year and return cover crops, organic mulch and your plant debris to the soil, and your plants are mostly growing well, you probably don’t need to add any other fertilizer to your garden. This alarmed me a bit. What about boron shortage, which happens here? Yes, if you are a farmer or market gardener, yields do matter and soil tests (free for commercial growers in Virginia) will be worthwhile. But for a home gardener, or a landscape gardener, yields might not be at the top of your list. Robert explains various tests, and gives his take on how useful they are. The information here can save a lot of confusion and wasted effort.
In the techniques chapter, the author explains the dramatic difference in available nitrogen in a cultivated garden and a no-till one. No-till can supply up to five times the nitrogen, because tilling adds more air into the soil, increasing the microbial activity, burning up the OM. There is a useful chart comparing the effects of fertilizer, compost and wood chips on the soil. We’ve all learned not to bury wood chips in the soil, where they use up the nitrogen while decomposing. But on the surface they can do wonders.
Crop rotation has come under scorn recently from commercial growers who are focused on maximizing yield and profit for their time on small areas of land. Sure, salad mix and baby spinach can rake in the money. But generations of farmers have learned to grow different types of crops each year in a particular spot. This can increase yields 10-25%, even though we are not sure why. Studies have shown it’s not simply nutrient availability. It could be pH changes freeing up more nutrients, or microbe biodiversity, or differing root growth granting access to more depth than the current crop alone can achieve. Rotated crops are more drought resistant and make better use of nitrogen. Research is needed.
As I was happily digesting this book I was brought short by this mnemonic that still puzzles me: “If you have trouble remembering whether P stands for phosphorus or potassium, remember that these nutrients are listed in alphabetical order. Phosphorus comes before potassium in the alphabet, and so P comes before K.” Um, K comes before P, last time I looked. Confusing.
Does rock dust add nutrients? No evidence, says Robert. Do not be beguiled by mineral products claiming to add 74 minerals to your soil. Plants might only use 20 of them. More is not better! Beware fad products such as biostimulants and probiotics. Plants cannot use vitamin B1. What about compost tea? Yes, it adds nutrients, but claims that the included microbes work wonders are not supported by science: test results are very mixed, including worse. Sometimes we are too gullible! Milk, molasses: they add nutrients but no special magic. Fermenting something cannot add nutrients – it could make some more available, although that isn’t proven either. The fungal and bacterial populations increase, but are the species nutritious ones or pathogenic ones?
The gardener’s goal is to farm healthy microbes, even though they are too small to see. Use the state of the soil and the health of the plants as indicators of the health of the microbes. Supply OM, water and you’re on the right track. It has been proved useful to add rhizobium legume inoculant if you haven’t grown legumes for some years. Fungal inoculation of soybeans in low phosphorus soil will be effective. Not otherwise.
The author’s general practice is to improve the soil environment to help existing microbes. There is a list of 7 general ways to do that. There is a whole chapter on increasing OM, using what’s local and cheap. Coir is a waste product, but its production causes environmental damage to local water supplies (large amounts of sodium have to be leached out).
Biochar, one of the new “Garden Wonders”, has claims to make big improvements to the soil food web. Most of the biochar studies have been conducted in labs, not on farms. Even then, 50% of the studies report higher yields, 20% report no change, and 30% report a decrease. There are probably better ways to spend your money!
The final section of the book is a set of worksheets and instructions to help gardeners improve the soil health where they are. This is a slow process, so start soon! Robert has also made the forms available on his website www.gardenfundamentals.com/soil-book-.... First assess your soil, then make an action plan, then record your progress.
I recommend this book for all sustainable/regenerative/organic gardeners and small-scale farmers, and even large-scale farmers who realize there are gaps in their understanding of soil science. This book is very accessible, user-friendly and full of soil-based common sense.
Author 33 books1 follower
April 6, 2020
I cannot recommend this book more highly!What sets this book apart from others on the subject is how accessible and practical it is to new and experienced gardeners alike. It is comprehensive and thorough and yet written in such a way that anyone can grasp the concepts without needing a science degree. Plus, you might actually find that you find the topic rather enjoyable! That takes the kind of skill, knowledge, and expertise that Pavlis consistently reveals on his website Garden Fundamentals.
Profile Image for Cary Morton.
989 reviews42 followers
April 10, 2020
I received a copy of this book directly from the author/publisher in exchange for an honest review.

Soil Science For Gardeners by Robert Pavlis is a fantastic book for gardeners, either beginners or those more experienced. It is a comprehensive guide to the science behind healthy soil and gets into the nitty-gritty of what is going on, even on the microscopic level. I was thoroughly impressed by the amount of knowledge and good advice presented, and would highly recommend this to anyone wanting to look further into the subject. The book was well written and easy to understand.
Profile Image for Leanna.
534 reviews8 followers
May 17, 2025
I appreciated him going over many of the fungi, pathogens, microbes, etc that are in the soil and I did like his information on mulching. I also learned a few new things about manure.

I may have misunderstood, but I thought I heard him say that gardeners, for the most part, wouldn't need to look at fertilizers because plants will grow without fertilizer. Farmers need to pay more attention to yields and therefore have their soil tested for deficiencies and then fertilize based on the deficiency. Then he goes into great mind numbing detail about all of the different formulations of fertilizers and how to figure out how much to apply. He also talks about minerals the same way. I did like him noting that you fertilize soil, not plants, but if the book is for gardeners, not farmers, why all the fertilizer details if they shouldn't be used? He also seems to poo-poo compost teas. He states that science doesn't support most of the applications gardeners are using like compost teas and azomite, etc. My experiences differ, so this book just made me scratch my head.

233 reviews
July 11, 2025
Interesting!

What I’ve learnt:
1) if you don’t have enough worms, that means you don’t have enough microbes- add more compost/organic matter (this is my issue at the allotment). But adding more and more compost if you already have worms is actually bad because it’ll mess up the balance of nutrients.
2) don’t worry about pH, it’s very hard to change, especially accidentally (eg too much woodchip will not make your soil more acidic). Adding lime etc is pointless (unless under direct instruction from a lab soil test)
3) avoid digging/tilling- it upsets the microbes and brings loads of weed seeds to the surface
4) proprietary feed inc tomato food is pointless. You can get the nutrients measured in the soil but it’s expensive and a bit pointless
5) mulch, mulch, mulch
6) don’t stand on your soil

So not exactly different to what I already knew, but I did learn about some of the science behind it
Profile Image for Snow.
22 reviews
March 29, 2023
A basic and readable soil science text. You can tell Pavlis had an axe to grind, and the book seems motivated by an obvious disdain for soil myths, old wives tales, and cargo cult gardening culture.

Opening the chapter on identifying soil problems, Pavlis writes,

Before you do anything in the garden, try to understand why you are doing it. What effect will it have? What problem are you solving? If you are not solving a problem, then don’t do it. Many standard gardening practices simply are not required.


This text provides enough information about soil structure and life's interactions with soil to identify problems that need solving and the practices that can address those specific problems; or at least it did for me.
Profile Image for Judy.
10 reviews
August 17, 2022
This book is a nice concise introduction to soil science. I learned a lot and the science doesn't get bogged in so much technical detail that the average layman's eyes glaze over. The only reason I gave it three stars is because of all the mistakes in the text that annoyed this nerd so much I started keeping track of them. There are about a dozen errors, including wrong words used, e.g. exasperate instead of exacerbate; misspelled words; numbers in the text that do not agree with the numbers in the chart it's referring to, and those are just the ones I noticed. I feel it's a disservice to authors to have their work published with errors that an attentive proofreader would have found.
1 review
March 10, 2023
Although I still learned some new information from this book regarding soil science, it provides no citations for its “evidence-based” claims. The author seems to have a lot of opinions against the pro-organic movement, and dismisses it as lacking scientific evidence. It is true that some organic methods are difficult to replicate in experiments, and other methods may not have the scientific backing yet - but this may change, as science continues to catch up. Garden advice should always be scrutinized, and may not be applicable to all locations, but for the author to make his big claims, he should have provided the scientific evidence he holds so highly.
Profile Image for Laura.
213 reviews2 followers
April 19, 2022
This book is well organized and focused on practical application. I think all gardeners could benefit from at least skimming it, although I'm going to have to go over it a few times because I have no talent for chemistry. Luckily you don't need a science background to understand most of it! As other reviewers have said it lacks sources, so it's a good introduction, but if you're serious about the subject you'll probably want another perspective.
Profile Image for Kenny.
18 reviews10 followers
May 29, 2024
this contains a lot of great info, mostly boiling down to "just add composted organic matter and don't touch your soil if you can help it". It's skeptical of common consensus that gets regurgitated everywhere, but take ALL of it with a grain of salt, the occasional typo tells me that it's unlikely this book was edited by anyone else and thus not "peer reviewed" (where peers could be other amateur gardeners). Hopefully I'm wrong!
2 reviews1 follower
September 22, 2021
Essential reading for every aspiring gardener who wants to understand what they are doing. Very easy to comprehend, great structuring of the text and occasionally witty too. A really enjoyable and deeply informative read, I love it! The lack of an extensive list of sources is a drawback and the only reason I can't give it five stars.
Profile Image for Kathy.
112 reviews9 followers
June 3, 2023
Gardening has made me interested in science. I do not want to take basic chemistry and biology classes. This book made me gain a better "applied' understanding of both. Some of it was still over my head but I picked up much informat ion that will make me a better gardener. I can see re-reading it in the future to hopefully understand more.
Profile Image for G. M. .
34 reviews5 followers
March 13, 2022
A little repetitive at times but I learned a lot about the importance of healthy soil and the main things to pay attention to as a gardener. I learned a lot, and I'm super glad I read this before starting my own garden. I would have probably done more damage then good with my garden prep.
Profile Image for Paul.
1,284 reviews29 followers
December 17, 2022
I didn't know you can be so opinionated and passionate about something so uncontroversial but clearly I was too ignorant of the complexities. Interesting to find out about the science but this is not a replacement for a technical book that could actually teach you about it.
Profile Image for Diane Wilkerson.
26 reviews6 followers
March 23, 2024
soil basics

A good primer on soil, its composition, the impact of organic materials, and fertilizers. Provides info on identification of the types of soils and improving various conditions. Easy to understand.
Profile Image for Özgür Takmaz.
258 reviews4 followers
August 23, 2020
-Origin of soil: Sand, Silt and Clay.
-Aggregation and compaction.
-You can't determine nutrient deficiency by looking at leaves.
-Rhizosphere
-Cut and drop cover crops.
-Roots penetrate 300 psi
Profile Image for Resa.
95 reviews2 followers
January 11, 2021
A wonderful resource for the new & experienced home and market gardener.
This will be a mainstay in my home library.
Profile Image for Joanne.
171 reviews6 followers
February 25, 2021
Well written by a scientist in an easy to understand style. He covers all areas of soil improvement for a garden and in so doing debunks many myths. Very informative and enlightening.
4 reviews2 followers
2021-booklist
March 8, 2021
Exactly as billed, with bonus garden-myth-busting.
Profile Image for Liz.
142 reviews3 followers
February 26, 2023
Not perfect, but pretty close. Highly recommended if you are interested in soil science.
Profile Image for Onni.
94 reviews
March 30, 2023
A very clear and informative place to start with understanding your garden soil.
Profile Image for Joe Waters.
19 reviews3 followers
April 21, 2023
A wonderfully informative book!

Be sure to read it with the author’s book on composting for a full understanding of your soil and how to improve it.
Profile Image for Terry.
434 reviews2 followers
June 30, 2025
As a home vegetable Gardner, this is more info than we will likely need. But still some good basic tips - more compost, manure and wood chip mulch.
Profile Image for Mechell.
71 reviews
November 1, 2025
Too technical for me. But if you can understand the sciencey stuff you might better appreciate it
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